data_4AYV
#
_model_server_result.job_id            Hj8PvJU3lpFXNF6Z7XGy0A 
_model_server_result.datetime_utc      '2025-02-17 16:52:50' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          4ayv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1258}' 
#
_entry.id    4AYV 
#
_exptl.entry_id    4AYV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              608.708 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '{Benzyl-[(S)-3-[((S)-1-carbamimidoyl-piperidin-3-ylmethyl)-carbamoyl]-2-(naphthalene-2-sulfonylamino)-propionyl]-amino}-acetic acid' 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            4AYV 
_cell.length_a            90.8 
_cell.length_b            90.8 
_cell.length_c            132.5 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4AYV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
disulf ? disulf1 A SG CYS 5 A CYS 9 1_555 B SG CYS 119 B CYS 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf2 B SG CYS 28 B CYS 28 1_555 B SG CYS 44 B CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
disulf ? disulf3 B SG CYS 173 B CYS 173 1_555 B SG CYS 187 B CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf4 B SG CYS 201 B CYS 201 1_555 B SG CYS 231 B CYS 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
covale ? covale1 B ND2 ASN 53 B ASN 53 1_555 E C1 NAG . B NAG 1259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
metalc ? metalc1 B O ARG 233 B ARG 233 1_555 F NA NA . B NA 1260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? 
metalc ? metalc2 B O LYS 236 B LYS 236 1_555 F NA NA . B NA 1260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc3 F NA NA . B NA 1260 1_555 H O HOH . B HOH 2043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc4 F NA NA . B NA 1260 1_555 H O HOH . B HOH 2044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.049 ? 
metalc ? metalc5 F NA NA . B NA 1260 1_555 H O HOH . B HOH 2046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? 
metalc ? metalc6 F NA NA . B NA 1260 1_555 H O HOH . B HOH 2050 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? 
#
_chem_comp.formula           'C30 H36 N6 O6 S' 
_chem_comp.formula_weight    608.708 
_chem_comp.id                9MQ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '{Benzyl-[(S)-3-[((S)-1-carbamimidoyl-piperidin-3-ylmethyl)-carbamoyl]-2-(naphthalene-2-sulfonylamino)-propionyl]-amino}-acetic acid' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
C1 C2 9MQ sing 1 n n 
C1 N3 9MQ sing 2 n n 
C1 C4 9MQ sing 3 n n 
C2 N5 9MQ sing 4 n n 
C2 O6 9MQ doub 5 n n 
N3 S7 9MQ sing 6 n n 
C4 C8 9MQ sing 7 n n 
N5 C9 9MQ sing 8 n n 
N5 C10 9MQ sing 9 n n 
S7 C11 9MQ sing 10 n n 
S7 O12 9MQ doub 11 n n 
S7 O13 9MQ doub 12 n n 
C8 N14 9MQ sing 13 n n 
C8 O15 9MQ doub 14 n n 
C9 C16 9MQ sing 15 n n 
C10 C17 9MQ sing 16 n n 
C11 C18 9MQ sing 17 n y 
C11 C19 9MQ doub 18 n y 
N14 C20 9MQ sing 19 n n 
C16 C21 9MQ sing 20 n y 
C16 C22 9MQ doub 21 n y 
C17 O23 9MQ sing 22 n n 
C17 O24 9MQ doub 23 n n 
C18 C25 9MQ doub 24 n y 
C19 C26 9MQ sing 25 n y 
C20 C27 9MQ sing 26 n n 
C21 C28 9MQ doub 27 n y 
C22 C29 9MQ sing 28 n y 
C25 C30 9MQ sing 29 n y 
C25 C31 9MQ sing 30 n y 
C26 C30 9MQ doub 31 n y 
C27 C32 9MQ sing 32 n n 
C27 C33 9MQ sing 33 n n 
C28 C34 9MQ sing 34 n y 
C29 C34 9MQ doub 35 n y 
C30 C35 9MQ sing 36 n y 
C31 C36 9MQ doub 37 n y 
C32 N37 9MQ sing 38 n n 
C33 C38 9MQ sing 39 n n 
C35 C39 9MQ doub 40 n y 
C36 C39 9MQ sing 41 n y 
N37 C40 9MQ sing 42 n n 
N37 C41 9MQ sing 43 n n 
C38 C40 9MQ sing 44 n n 
C41 N42 9MQ doub 45 n n 
C41 N43 9MQ sing 46 n n 
C1 H1 9MQ sing 47 n n 
N3 H3 9MQ sing 48 n n 
C4 H41C 9MQ sing 49 n n 
C4 H42C 9MQ sing 50 n n 
C9 H91C 9MQ sing 51 n n 
C9 H92C 9MQ sing 52 n n 
C10 H101 9MQ sing 53 n n 
C10 H102 9MQ sing 54 n n 
N14 H14 9MQ sing 55 n n 
C18 H18 9MQ sing 56 n n 
C19 H19 9MQ sing 57 n n 
C20 H201 9MQ sing 58 n n 
C20 H202 9MQ sing 59 n n 
C21 H21 9MQ sing 60 n n 
C22 H22 9MQ sing 61 n n 
O23 H23 9MQ sing 62 n n 
C26 H26 9MQ sing 63 n n 
C27 H27 9MQ sing 64 n n 
C28 H28 9MQ sing 65 n n 
C29 H29 9MQ sing 66 n n 
C31 H31 9MQ sing 67 n n 
C32 H321 9MQ sing 68 n n 
C32 H322 9MQ sing 69 n n 
C33 H331 9MQ sing 70 n n 
C33 H332 9MQ sing 71 n n 
C34 H34 9MQ sing 72 n n 
C35 H35 9MQ sing 73 n n 
C36 H36 9MQ sing 74 n n 
C38 H381 9MQ sing 75 n n 
C38 H382 9MQ sing 76 n n 
C39 H39 9MQ sing 77 n n 
C40 H401 9MQ sing 78 n n 
C40 H402 9MQ sing 79 n n 
N42 H42 9MQ sing 80 n n 
N43 H431 9MQ sing 81 n n 
N43 H432 9MQ sing 82 n n 
#
_atom_sites.entry_id                     4AYV 
_atom_sites.fract_transf_matrix[1][1]    0.011013 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011013 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.007547 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
D 4 9MQ B 1 1258 1258 9MQ 9MQ . 
E 5 NAG B 1 1259 1259 NAG NAG . 
F 6 NA B 1 1260 1260 NA NA . 
G 7 HOH A 1 2001 2001 HOH HOH . 
G 7 HOH A 2 2002 2002 HOH HOH . 
G 7 HOH A 3 2003 2003 HOH HOH . 
G 7 HOH A 4 2004 2004 HOH HOH . 
G 7 HOH A 5 2005 2005 HOH HOH . 
H 7 HOH B 1 2001 2001 HOH HOH . 
H 7 HOH B 2 2002 2002 HOH HOH . 
H 7 HOH B 3 2003 2003 HOH HOH . 
H 7 HOH B 4 2004 2004 HOH HOH . 
H 7 HOH B 5 2005 2005 HOH HOH . 
H 7 HOH B 6 2006 2006 HOH HOH . 
H 7 HOH B 7 2007 2007 HOH HOH . 
H 7 HOH B 8 2008 2008 HOH HOH . 
H 7 HOH B 9 2009 2009 HOH HOH . 
H 7 HOH B 10 2010 2010 HOH HOH . 
H 7 HOH B 11 2011 2011 HOH HOH . 
H 7 HOH B 12 2012 2012 HOH HOH . 
H 7 HOH B 13 2013 2013 HOH HOH . 
H 7 HOH B 14 2014 2014 HOH HOH . 
H 7 HOH B 15 2015 2015 HOH HOH . 
H 7 HOH B 16 2016 2016 HOH HOH . 
H 7 HOH B 17 2017 2017 HOH HOH . 
H 7 HOH B 18 2018 2018 HOH HOH . 
H 7 HOH B 19 2019 2019 HOH HOH . 
H 7 HOH B 20 2020 2020 HOH HOH . 
H 7 HOH B 21 2021 2021 HOH HOH . 
H 7 HOH B 22 2022 2022 HOH HOH . 
H 7 HOH B 23 2023 2023 HOH HOH . 
H 7 HOH B 24 2024 2024 HOH HOH . 
H 7 HOH B 25 2025 2025 HOH HOH . 
H 7 HOH B 26 2026 2026 HOH HOH . 
H 7 HOH B 27 2027 2027 HOH HOH . 
H 7 HOH B 28 2028 2028 HOH HOH . 
H 7 HOH B 29 2029 2029 HOH HOH . 
H 7 HOH B 30 2030 2030 HOH HOH . 
H 7 HOH B 31 2031 2031 HOH HOH . 
H 7 HOH B 32 2032 2032 HOH HOH . 
H 7 HOH B 33 2033 2033 HOH HOH . 
H 7 HOH B 34 2034 2034 HOH HOH . 
H 7 HOH B 35 2035 2035 HOH HOH . 
H 7 HOH B 36 2036 2036 HOH HOH . 
H 7 HOH B 37 2037 2037 HOH HOH . 
H 7 HOH B 38 2038 2038 HOH HOH . 
H 7 HOH B 39 2039 2039 HOH HOH . 
H 7 HOH B 40 2040 2040 HOH HOH . 
H 7 HOH B 41 2041 2041 HOH HOH . 
H 7 HOH B 42 2042 2042 HOH HOH . 
H 7 HOH B 43 2043 2043 HOH HOH . 
H 7 HOH B 44 2044 2044 HOH HOH . 
H 7 HOH B 45 2045 2045 HOH HOH . 
H 7 HOH B 46 2046 2046 HOH HOH . 
H 7 HOH B 47 2047 2047 HOH HOH . 
H 7 HOH B 48 2048 2048 HOH HOH . 
H 7 HOH B 49 2049 2049 HOH HOH . 
H 7 HOH B 50 2050 2050 HOH HOH . 
H 7 HOH B 51 2051 2051 HOH HOH . 
I 7 HOH D 1 2001 2001 HOH HOH . 
I 7 HOH D 2 2002 2002 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 C C20 9MQ . . . D 4 29.522 17.638 23.689 1 23.78 ? C20 9MQ 1258 B 1 
HETATM 2 C C27 9MQ . . . D 4 30.839 18.369 24.041 1 23.75 ? C27 9MQ 1258 B 1 
HETATM 3 C C32 9MQ . . . D 4 31.355 18.023 25.455 1 23.17 ? C32 9MQ 1258 B 1 
HETATM 4 C C33 9MQ . . . D 4 31.939 18.05 22.978 1 23.35 ? C33 9MQ 1258 B 1 
HETATM 5 N N37 9MQ . . . D 4 32.579 18.878 25.645 1 22.96 ? N37 9MQ 1258 B 1 
HETATM 6 C C38 9MQ . . . D 4 33.147 18.946 23.217 1 22.9 ? C38 9MQ 1258 B 1 
HETATM 7 C C40 9MQ . . . D 4 33.713 18.696 24.647 1 23.08 ? C40 9MQ 1258 B 1 
HETATM 8 C C41 9MQ . . . D 4 32.427 20.094 26.301 1 22.36 ? C41 9MQ 1258 B 1 
HETATM 9 N N42 9MQ . . . D 4 33.513 20.85 26.342 1 23.11 ? N42 9MQ 1258 B 1 
HETATM 10 N N43 9MQ . . . D 4 31.269 20.421 26.812 1 21.75 ? N43 9MQ 1258 B 1 
HETATM 11 N N3 9MQ . . . D 4 29.75 13.418 26.661 1 33.17 ? N3 9MQ 1258 B 1 
HETATM 12 C C1 9MQ . . . D 4 29.893 13.13 25.275 1 30.29 ? C1 9MQ 1258 B 1 
HETATM 13 C C2 9MQ . . . D 4 31.307 13.59 24.861 1 31.36 ? C2 9MQ 1258 B 1 
HETATM 14 O O6 9MQ . . . D 4 31.925 14.432 25.546 1 31.67 ? O6 9MQ 1258 B 1 
HETATM 15 C C4 9MQ . . . D 4 28.864 13.902 24.4 1 26.86 ? C4 9MQ 1258 B 1 
HETATM 16 C C8 9MQ . . . D 4 28.834 15.408 24.557 1 25.33 ? C8 9MQ 1258 B 1 
HETATM 17 O O15 9MQ . . . D 4 28.216 15.978 25.484 1 26.22 ? O15 9MQ 1258 B 1 
HETATM 18 N N14 9MQ . . . D 4 29.55 16.152 23.598 1 23.87 ? N14 9MQ 1258 B 1 
HETATM 19 S S7 9MQ . . . D 4 29.31 12.275 27.758 1 35.77 ? S7 9MQ 1258 B 1 
HETATM 20 O O13 9MQ . . . D 4 28.36 11.426 27.148 1 35.32 ? O13 9MQ 1258 B 1 
HETATM 21 O O12 9MQ . . . D 4 29.063 13.062 28.954 1 33.95 ? O12 9MQ 1258 B 1 
HETATM 22 C C18 9MQ . . . D 4 30.764 10.06 27.313 1 34.48 ? C18 9MQ 1258 B 1 
HETATM 23 C C11 9MQ . . . D 4 30.655 11.305 27.931 1 35.07 ? C11 9MQ 1258 B 1 
HETATM 24 C C19 9MQ . . . D 4 31.732 11.777 28.759 1 34.57 ? C19 9MQ 1258 B 1 
HETATM 25 C C26 9MQ . . . D 4 32.863 11.047 28.966 1 35.06 ? C26 9MQ 1258 B 1 
HETATM 26 C C35 9MQ . . . D 4 34.177 9.006 28.594 1 34.49 ? C35 9MQ 1258 B 1 
HETATM 27 C C39 9MQ . . . D 4 34.283 7.769 28.009 1 36.28 ? C39 9MQ 1258 B 1 
HETATM 28 C C36 9MQ . . . D 4 33.24 7.241 27.176 1 37.45 ? C36 9MQ 1258 B 1 
HETATM 29 C C31 9MQ . . . D 4 32.088 7.972 26.933 1 36.59 ? C31 9MQ 1258 B 1 
HETATM 30 C C25 9MQ . . . D 4 31.94 9.266 27.525 1 36 ? C25 9MQ 1258 B 1 
HETATM 31 C C30 9MQ . . . D 4 33.003 9.773 28.362 1 35.16 ? C30 9MQ 1258 B 1 
HETATM 32 N N5 9MQ . . . D 4 31.868 13.041 23.707 1 31 ? N5 9MQ 1258 B 1 
HETATM 33 C C9 9MQ . . . D 4 31.181 11.955 22.933 1 31.33 ? C9 9MQ 1258 B 1 
HETATM 34 C C10 9MQ . . . D 4 33.098 13.59 23.112 1 29.94 ? C10 9MQ 1258 B 1 
HETATM 35 C C16 9MQ . . . D 4 32.127 10.819 22.731 1 32.24 ? C16 9MQ 1258 B 1 
HETATM 36 C C17 9MQ . . . D 4 32.677 14.542 21.998 1 29.5 ? C17 9MQ 1258 B 1 
HETATM 37 C C21 9MQ . . . D 4 32.74 10.195 23.855 1 33.26 ? C21 9MQ 1258 B 1 
HETATM 38 C C22 9MQ . . . D 4 32.415 10.404 21.439 1 31.55 ? C22 9MQ 1258 B 1 
HETATM 39 O O23 9MQ . . . D 4 33.612 14.684 21.068 1 28.67 ? O23 9MQ 1258 B 1 
HETATM 40 O O24 9MQ . . . D 4 31.623 15.137 21.867 1 29.69 ? O24 9MQ 1258 B 1 
HETATM 41 C C28 9MQ . . . D 4 33.656 9.149 23.674 1 34.16 ? C28 9MQ 1258 B 1 
HETATM 42 C C29 9MQ . . . D 4 33.335 9.35 21.252 1 33.58 ? C29 9MQ 1258 B 1 
HETATM 43 C C34 9MQ . . . D 4 33.959 8.722 22.353 1 34.28 ? C34 9MQ 1258 B 1 
#
_model_server_stats.io_time_ms              49 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#