data_5NMD
#
_model_server_result.job_id            wEiYDSeEr7tNZcKUUQEIIA 
_model_server_result.datetime_utc      '2024-10-11 04:31:42' 
_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          5nmd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":301}' 
#
_entry.id    5NMD 
#
_exptl.entry_id    5NMD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              62.068 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-ETHANEDIOL 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.16 
_cell.angle_gamma         90 
_cell.entry_id            5NMD 
_cell.length_a            87.47 
_cell.length_b            50.62 
_cell.length_c            114.31 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5NMD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 software_defined_assembly 1 
PISA dimeric 2 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,H,I,N,O 1 1 
C,D,J,K,L,M,P,Q 2 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 E N N 
? 3 G N N 
? 3 H N N 
? 3 J N 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 22 A CYS 23 1_555 A SG CYS 88 A CYS 89 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.076 ? 
disulf ? disulf2 A SG CYS 22 A CYS 23 1_555 A SG CYS 88 A CYS 89 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.133 ? 
disulf ? disulf3 A SG CYS 133 A CYS 134 1_555 A SG CYS 183 A CYS 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
disulf ? disulf4 A SG CYS 158 A CYS 159 1_555 B SG CYS 169 B CYS 169 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.106 ? 
disulf ? disulf5 A SG CYS 158 A CYS 159 1_555 B SG CYS 169 B CYS 169 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.078 ? 
disulf ? disulf6 B SG CYS 23 B CYS 23 1_555 B SG CYS 91 B CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf7 B SG CYS 143 B CYS 143 1_555 B SG CYS 208 B CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
disulf ? disulf8 C SG CYS 22 C CYS 23 1_555 C SG CYS 88 C CYS 89 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.1 ? 
disulf ? disulf9 C SG CYS 22 C CYS 23 1_555 C SG CYS 88 C CYS 89 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.117 ? 
disulf ? disulf10 C SG CYS 133 C CYS 134 1_555 C SG CYS 183 C CYS 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
disulf ? disulf11 C SG CYS 158 C CYS 159 1_555 D SG CYS 169 D CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
disulf ? disulf12 D SG CYS 23 D CYS 23 1_555 D SG CYS 91 D CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
disulf ? disulf13 D SG CYS 143 D CYS 143 1_555 D SG CYS 208 D CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? 
#
_chem_comp.formula           'C2 H6 O2' 
_chem_comp.formula_weight    62.068 
_chem_comp.id                EDO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,2-ETHANEDIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'ETHYLENE GLYCOL' 
#
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 O1 EDO sing 83 n n 
C1 C2 EDO sing 84 n n 
C1 H11 EDO sing 85 n n 
C1 H12 EDO sing 86 n n 
O1 HO1 EDO sing 87 n n 
C2 O2 EDO sing 88 n n 
C2 H21 EDO sing 89 n n 
C2 H22 EDO sing 90 n n 
O2 HO2 EDO sing 91 n n 
#
_atom_sites.entry_id                     5NMD 
_atom_sites.fract_transf_matrix[1][1]    0.011432 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000032 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019755 
_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]    0.008748 
_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
E 3 EDO A 1 301 302 EDO EDO . 
F 4 SO4 A 1 302 314 SO4 SO4 . 
G 3 EDO B 1 301 301 EDO EDO . 
H 3 EDO B 1 302 303 EDO EDO . 
I 4 SO4 B 1 303 315 SO4 SO4 . 
J 3 EDO C 1 301 304 EDO EDO . 
K 4 SO4 C 1 302 312 SO4 SO4 . 
L 4 SO4 D 1 301 311 SO4 SO4 . 
M 4 SO4 D 1 302 313 SO4 SO4 . 
N 5 HOH A 1 401 557 HOH HOH . 
N 5 HOH A 2 402 496 HOH HOH . 
N 5 HOH A 3 403 547 HOH HOH . 
N 5 HOH A 4 404 603 HOH HOH . 
N 5 HOH A 5 405 569 HOH HOH . 
N 5 HOH A 6 406 479 HOH HOH . 
N 5 HOH A 7 407 497 HOH HOH . 
N 5 HOH A 8 408 430 HOH HOH . 
N 5 HOH A 9 409 409 HOH HOH . 
N 5 HOH A 10 410 413 HOH HOH . 
N 5 HOH A 11 411 600 HOH HOH . 
N 5 HOH A 12 412 481 HOH HOH . 
N 5 HOH A 13 413 538 HOH HOH . 
N 5 HOH A 14 414 492 HOH HOH . 
N 5 HOH A 15 415 558 HOH HOH . 
N 5 HOH A 16 416 401 HOH HOH . 
N 5 HOH A 17 417 406 HOH HOH . 
N 5 HOH A 18 418 428 HOH HOH . 
N 5 HOH A 19 419 425 HOH HOH . 
N 5 HOH A 20 420 415 HOH HOH . 
N 5 HOH A 21 421 550 HOH HOH . 
N 5 HOH A 22 422 437 HOH HOH . 
N 5 HOH A 23 423 476 HOH HOH . 
N 5 HOH A 24 424 549 HOH HOH . 
N 5 HOH A 25 425 473 HOH HOH . 
N 5 HOH A 26 426 542 HOH HOH . 
N 5 HOH A 27 427 507 HOH HOH . 
N 5 HOH A 28 428 553 HOH HOH . 
N 5 HOH A 29 429 568 HOH HOH . 
N 5 HOH A 30 430 510 HOH HOH . 
N 5 HOH A 31 431 519 HOH HOH . 
N 5 HOH A 32 432 593 HOH HOH . 
N 5 HOH A 33 433 500 HOH HOH . 
N 5 HOH A 34 434 554 HOH HOH . 
N 5 HOH A 35 435 608 HOH HOH . 
N 5 HOH A 36 436 499 HOH HOH . 
N 5 HOH A 37 437 491 HOH HOH . 
N 5 HOH A 38 438 581 HOH HOH . 
N 5 HOH A 39 439 539 HOH HOH . 
O 5 HOH B 1 401 532 HOH HOH . 
O 5 HOH B 2 402 424 HOH HOH . 
O 5 HOH B 3 403 572 HOH HOH . 
O 5 HOH B 4 404 461 HOH HOH . 
O 5 HOH B 5 405 498 HOH HOH . 
O 5 HOH B 6 406 588 HOH HOH . 
O 5 HOH B 7 407 526 HOH HOH . 
O 5 HOH B 8 408 414 HOH HOH . 
O 5 HOH B 9 409 583 HOH HOH . 
O 5 HOH B 10 410 524 HOH HOH . 
O 5 HOH B 11 411 489 HOH HOH . 
O 5 HOH B 12 412 531 HOH HOH . 
O 5 HOH B 13 413 426 HOH HOH . 
O 5 HOH B 14 414 410 HOH HOH . 
O 5 HOH B 15 415 530 HOH HOH . 
O 5 HOH B 16 416 567 HOH HOH . 
O 5 HOH B 17 417 453 HOH HOH . 
O 5 HOH B 18 418 573 HOH HOH . 
O 5 HOH B 19 419 487 HOH HOH . 
O 5 HOH B 20 420 552 HOH HOH . 
O 5 HOH B 21 421 517 HOH HOH . 
O 5 HOH B 22 422 405 HOH HOH . 
O 5 HOH B 23 423 493 HOH HOH . 
O 5 HOH B 24 424 575 HOH HOH . 
O 5 HOH B 25 425 584 HOH HOH . 
O 5 HOH B 26 426 416 HOH HOH . 
O 5 HOH B 27 427 454 HOH HOH . 
O 5 HOH B 28 428 541 HOH HOH . 
O 5 HOH B 29 429 566 HOH HOH . 
O 5 HOH B 30 430 412 HOH HOH . 
O 5 HOH B 31 431 438 HOH HOH . 
O 5 HOH B 32 432 540 HOH HOH . 
O 5 HOH B 33 433 570 HOH HOH . 
O 5 HOH B 34 434 490 HOH HOH . 
O 5 HOH B 35 435 590 HOH HOH . 
O 5 HOH B 36 436 528 HOH HOH . 
O 5 HOH B 37 437 457 HOH HOH . 
O 5 HOH B 38 438 571 HOH HOH . 
O 5 HOH B 39 439 480 HOH HOH . 
O 5 HOH B 40 440 439 HOH HOH . 
O 5 HOH B 41 441 595 HOH HOH . 
O 5 HOH B 42 442 460 HOH HOH . 
O 5 HOH B 43 443 418 HOH HOH . 
O 5 HOH B 44 444 445 HOH HOH . 
O 5 HOH B 45 445 597 HOH HOH . 
O 5 HOH B 46 446 564 HOH HOH . 
O 5 HOH B 47 447 520 HOH HOH . 
O 5 HOH B 48 448 501 HOH HOH . 
O 5 HOH B 49 449 577 HOH HOH . 
O 5 HOH B 50 450 431 HOH HOH . 
O 5 HOH B 51 451 527 HOH HOH . 
O 5 HOH B 52 452 576 HOH HOH . 
O 5 HOH B 53 453 525 HOH HOH . 
O 5 HOH B 54 454 443 HOH HOH . 
O 5 HOH B 55 455 433 HOH HOH . 
O 5 HOH B 56 456 556 HOH HOH . 
O 5 HOH B 57 457 403 HOH HOH . 
O 5 HOH B 58 458 423 HOH HOH . 
O 5 HOH B 59 459 580 HOH HOH . 
O 5 HOH B 60 460 402 HOH HOH . 
O 5 HOH B 61 461 503 HOH HOH . 
O 5 HOH B 62 462 484 HOH HOH . 
O 5 HOH B 63 463 404 HOH HOH . 
O 5 HOH B 64 464 562 HOH HOH . 
O 5 HOH B 65 465 427 HOH HOH . 
O 5 HOH B 66 466 609 HOH HOH . 
O 5 HOH B 67 467 470 HOH HOH . 
O 5 HOH B 68 468 419 HOH HOH . 
O 5 HOH B 69 469 555 HOH HOH . 
O 5 HOH B 70 470 452 HOH HOH . 
O 5 HOH B 71 471 606 HOH HOH . 
O 5 HOH B 72 472 494 HOH HOH . 
O 5 HOH B 73 473 466 HOH HOH . 
O 5 HOH B 74 474 447 HOH HOH . 
O 5 HOH B 75 475 586 HOH HOH . 
O 5 HOH B 76 476 486 HOH HOH . 
O 5 HOH B 77 477 450 HOH HOH . 
O 5 HOH B 78 478 607 HOH HOH . 
O 5 HOH B 79 479 482 HOH HOH . 
O 5 HOH B 80 480 422 HOH HOH . 
O 5 HOH B 81 481 594 HOH HOH . 
O 5 HOH B 82 482 478 HOH HOH . 
O 5 HOH B 83 483 605 HOH HOH . 
O 5 HOH B 84 484 446 HOH HOH . 
O 5 HOH B 85 485 434 HOH HOH . 
O 5 HOH B 86 486 516 HOH HOH . 
O 5 HOH B 87 487 444 HOH HOH . 
O 5 HOH B 88 488 435 HOH HOH . 
O 5 HOH B 89 489 464 HOH HOH . 
O 5 HOH B 90 490 579 HOH HOH . 
O 5 HOH B 91 491 574 HOH HOH . 
O 5 HOH B 92 492 587 HOH HOH . 
O 5 HOH B 93 493 523 HOH HOH . 
O 5 HOH B 94 494 545 HOH HOH . 
O 5 HOH B 95 495 611 HOH HOH . 
O 5 HOH B 96 496 610 HOH HOH . 
O 5 HOH B 97 497 589 HOH HOH . 
O 5 HOH B 98 498 522 HOH HOH . 
O 5 HOH B 99 499 612 HOH HOH . 
O 5 HOH B 100 500 598 HOH HOH . 
O 5 HOH B 101 501 515 HOH HOH . 
P 5 HOH C 1 401 521 HOH HOH . 
P 5 HOH C 2 402 469 HOH HOH . 
P 5 HOH C 3 403 472 HOH HOH . 
P 5 HOH C 4 404 511 HOH HOH . 
P 5 HOH C 5 405 591 HOH HOH . 
P 5 HOH C 6 406 440 HOH HOH . 
P 5 HOH C 7 407 534 HOH HOH . 
P 5 HOH C 8 408 441 HOH HOH . 
P 5 HOH C 9 409 436 HOH HOH . 
P 5 HOH C 10 410 560 HOH HOH . 
P 5 HOH C 11 411 561 HOH HOH . 
P 5 HOH C 12 412 585 HOH HOH . 
P 5 HOH C 13 413 408 HOH HOH . 
P 5 HOH C 14 414 485 HOH HOH . 
P 5 HOH C 15 415 582 HOH HOH . 
P 5 HOH C 16 416 599 HOH HOH . 
P 5 HOH C 17 417 432 HOH HOH . 
P 5 HOH C 18 418 459 HOH HOH . 
P 5 HOH C 19 419 417 HOH HOH . 
P 5 HOH C 20 420 455 HOH HOH . 
P 5 HOH C 21 421 471 HOH HOH . 
P 5 HOH C 22 422 596 HOH HOH . 
P 5 HOH C 23 423 508 HOH HOH . 
P 5 HOH C 24 424 533 HOH HOH . 
P 5 HOH C 25 425 465 HOH HOH . 
P 5 HOH C 26 426 483 HOH HOH . 
P 5 HOH C 27 427 505 HOH HOH . 
P 5 HOH C 28 428 546 HOH HOH . 
P 5 HOH C 29 429 544 HOH HOH . 
Q 5 HOH D 1 401 529 HOH HOH . 
Q 5 HOH D 2 402 421 HOH HOH . 
Q 5 HOH D 3 403 578 HOH HOH . 
Q 5 HOH D 4 404 565 HOH HOH . 
Q 5 HOH D 5 405 488 HOH HOH . 
Q 5 HOH D 6 406 512 HOH HOH . 
Q 5 HOH D 7 407 506 HOH HOH . 
Q 5 HOH D 8 408 495 HOH HOH . 
Q 5 HOH D 9 409 514 HOH HOH . 
Q 5 HOH D 10 410 468 HOH HOH . 
Q 5 HOH D 11 411 451 HOH HOH . 
Q 5 HOH D 12 412 477 HOH HOH . 
Q 5 HOH D 13 413 604 HOH HOH . 
Q 5 HOH D 14 414 458 HOH HOH . 
Q 5 HOH D 15 415 442 HOH HOH . 
Q 5 HOH D 16 416 551 HOH HOH . 
Q 5 HOH D 17 417 513 HOH HOH . 
Q 5 HOH D 18 418 559 HOH HOH . 
Q 5 HOH D 19 419 448 HOH HOH . 
Q 5 HOH D 20 420 407 HOH HOH . 
Q 5 HOH D 21 421 475 HOH HOH . 
Q 5 HOH D 22 422 467 HOH HOH . 
Q 5 HOH D 23 423 411 HOH HOH . 
Q 5 HOH D 24 424 536 HOH HOH . 
Q 5 HOH D 25 425 462 HOH HOH . 
Q 5 HOH D 26 426 509 HOH HOH . 
Q 5 HOH D 27 427 592 HOH HOH . 
Q 5 HOH D 28 428 504 HOH HOH . 
Q 5 HOH D 29 429 548 HOH HOH . 
Q 5 HOH D 30 430 463 HOH HOH . 
Q 5 HOH D 31 431 537 HOH HOH . 
Q 5 HOH D 32 432 449 HOH HOH . 
Q 5 HOH D 33 433 535 HOH HOH . 
Q 5 HOH D 34 434 429 HOH HOH . 
Q 5 HOH D 35 435 474 HOH HOH . 
Q 5 HOH D 36 436 502 HOH HOH . 
Q 5 HOH D 37 437 420 HOH HOH . 
Q 5 HOH D 38 438 563 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 C1 EDO . . . E 3 35.616 -5.763 14.815 1 57.51 ? C1 EDO 301 A 1 
HETATM 2 O O1 EDO . . . E 3 35.535 -5.272 16.16 1 49.43 ? O1 EDO 301 A 1 
HETATM 3 C C2 EDO . . . E 3 36.146 -4.707 13.837 1 57.99 ? C2 EDO 301 A 1 
HETATM 4 O O2 EDO . . . E 3 37.531 -4.36 14.072 1 52.53 ? O2 EDO 301 A 1 
#
_model_server_stats.io_time_ms              21 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           300 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           4 
#