1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Sorimachi, K. Le Gal-Coeffet, M.-F. Williamson, G. Archer, D.B. Williamson, M.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C6 H12 O6 180.156 alpha-D-glucopyranose D-saccharide, alpha linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking UK Structure STRUE6 2005 0969-2126 5 647 661 10.1016/S0969-2126(97)00220-7 9195884 Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to beta-cyclodextrin. 1997 UK J.Mol.Biol. JMOBAK 0070 0022-2836 259 970 Solution Structure of the Granular Starch Binding Domain of Glucoamylase from Aspergillus Niger by Nuclear Magnetic Resonance Spectroscopy 1996 GLC B 2 HAS WRONG CHIRALITY AT ATOM C1 GLC B 5 HAS WRONG CHIRALITY AT ATOM C1 GLC C 6 HAS WRONG CHIRALITY AT ATOM C1 GLC C 7 HAS WRONG CHIRALITY AT ATOM C1 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 11884.820 GLUCOAMYLASE 3.2.1.3 BINDING DOMAIN, RESIDUES 509 - 616 1 man polymer 1153.001 Cycloheptakis-(1-4)-(alpha-D-glucopyranose) 2 man branched 1,4-ALPHA-D-GLUCAN GLUCOHYDROLASE beta-cyclodextrin no no CTTPTAVAVTFDLTATTTYGENIYLVGSISQLGDWETSDGIALSADKYTSSDPLWYVTVTLPAGESFEYKFIRIESDDSV EWESDPNREYTVPQACGTSTATVTDTWR CTTPTAVAVTFDLTATTTYGENIYLVGSISQLGDWETSDGIALSADKYTSSDPLWYVTVTLPAGESFEYKFIRIESDDSV EWESDPNREYTVPQACGTSTATVTDTWR A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Aspergillus AB4.1 Aspergillus sample 5061 Aspergillus niger A. NIGER GLAA 5061 Aspergillus niger PIGF atom_site chem_comp database_PDB_caveat entity entity_name_com pdbx_branch_scheme pdbx_chem_comp_identifier pdbx_database_status pdbx_entity_branch pdbx_entity_branch_descriptor pdbx_entity_branch_link pdbx_entity_branch_list pdbx_entity_nonpoly pdbx_molecule_features pdbx_nmr_refine pdbx_nmr_software pdbx_nonpoly_scheme pdbx_struct_assembly pdbx_struct_assembly_prop pdbx_struct_oper_list pdbx_validate_chiral pdbx_validate_close_contact struct_asym struct_conn struct_site struct_site_gen repository Initial release Carbohydrate remediation repository Remediation Version format compliance Version format compliance Advisory Atomic model Data collection Derived calculations Non-polymer description Other Refinement description Structure summary 1 0 1997-07-07 1 1 2008-03-24 1 2 2011-07-13 2 0 2020-07-29 _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.label_asym_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_entity_id _atom_site.pdbx_PDB_ins_code _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.type _pdbx_database_status.process_site _pdbx_nmr_refine.details _pdbx_nmr_software.version _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id A GLC 1 n B GLC 1 A GLC 2 n B GLC 2 A GLC 3 n B GLC 3 A GLC 4 n B GLC 4 A GLC 5 n B GLC 5 A GLC 6 n B GLC 6 A GLC 7 n B GLC 7 A GLC 617 n C GLC 1 A GLC 618 n C GLC 2 A GLC 619 n C GLC 3 A GLC 620 n C GLC 4 A GLC 621 n C GLC 5 A GLC 622 n C GLC 6 A GLC 623 n C GLC 7 DGlcpa a-D-glucopyranose a-D-Glcp Glc Y BNL 1997-02-10 REL REL oligosaccharide WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1 2 PDB2Glycan 1.1.0 WURCS C1 O4 GLC GLC 1 7 2 O1 HO4 sing C1 O4 GLC GLC 2 1 2 O1 HO4 sing C1 O4 GLC GLC 3 2 2 O1 HO4 sing C1 O4 GLC GLC 4 3 2 O1 HO4 sing C1 O4 GLC GLC 5 4 2 O1 HO4 sing C1 O4 GLC GLC 6 5 2 O1 HO4 sing C1 O4 GLC GLC 7 6 2 O1 HO4 sing n n n n n n n Drug delivery cyclic oligosaccharide beta-cyclodextrin Oligosaccharide RANDOM FROM 81 GOOD STRUCTURES 100 1 15N-EDITED TOCSY NOESY 5.7 310 K THE VALUES SHOWN IN THE TEMPERATURE FACTOR FIELD ARE ATOMIC RMSD VALUES OF 41 STRUCTURES TO THE UNMINIMIZED AVERAGE STRUCTURE. simulated annealing BRUNGER refinement X-PLOR structure solution X-PLOR 500 Bruker AMX 500 CYS 509 n 1 CYS 509 A THR 510 n 2 THR 510 A THR 511 n 3 THR 511 A PRO 512 n 4 PRO 512 A THR 513 n 5 THR 513 A ALA 514 n 6 ALA 514 A VAL 515 n 7 VAL 515 A ALA 516 n 8 ALA 516 A VAL 517 n 9 VAL 517 A THR 518 n 10 THR 518 A PHE 519 n 11 PHE 519 A ASP 520 n 12 ASP 520 A LEU 521 n 13 LEU 521 A THR 522 n 14 THR 522 A ALA 523 n 15 ALA 523 A THR 524 n 16 THR 524 A THR 525 n 17 THR 525 A THR 526 n 18 THR 526 A TYR 527 n 19 TYR 527 A GLY 528 n 20 GLY 528 A GLU 529 n 21 GLU 529 A ASN 530 n 22 ASN 530 A ILE 531 n 23 ILE 531 A TYR 532 n 24 TYR 532 A LEU 533 n 25 LEU 533 A VAL 534 n 26 VAL 534 A GLY 535 n 27 GLY 535 A SER 536 n 28 SER 536 A ILE 537 n 29 ILE 537 A SER 538 n 30 SER 538 A GLN 539 n 31 GLN 539 A LEU 540 n 32 LEU 540 A GLY 541 n 33 GLY 541 A ASP 542 n 34 ASP 542 A TRP 543 n 35 TRP 543 A GLU 544 n 36 GLU 544 A THR 545 n 37 THR 545 A SER 546 n 38 SER 546 A ASP 547 n 39 ASP 547 A GLY 548 n 40 GLY 548 A ILE 549 n 41 ILE 549 A ALA 550 n 42 ALA 550 A LEU 551 n 43 LEU 551 A SER 552 n 44 SER 552 A ALA 553 n 45 ALA 553 A ASP 554 n 46 ASP 554 A LYS 555 n 47 LYS 555 A TYR 556 n 48 TYR 556 A THR 557 n 49 THR 557 A SER 558 n 50 SER 558 A SER 559 n 51 SER 559 A ASP 560 n 52 ASP 560 A PRO 561 n 53 PRO 561 A LEU 562 n 54 LEU 562 A TRP 563 n 55 TRP 563 A TYR 564 n 56 TYR 564 A VAL 565 n 57 VAL 565 A THR 566 n 58 THR 566 A VAL 567 n 59 VAL 567 A THR 568 n 60 THR 568 A LEU 569 n 61 LEU 569 A PRO 570 n 62 PRO 570 A ALA 571 n 63 ALA 571 A GLY 572 n 64 GLY 572 A GLU 573 n 65 GLU 573 A SER 574 n 66 SER 574 A PHE 575 n 67 PHE 575 A GLU 576 n 68 GLU 576 A TYR 577 n 69 TYR 577 A LYS 578 n 70 LYS 578 A PHE 579 n 71 PHE 579 A ILE 580 n 72 ILE 580 A ARG 581 n 73 ARG 581 A ILE 582 n 74 ILE 582 A GLU 583 n 75 GLU 583 A SER 584 n 76 SER 584 A ASP 585 n 77 ASP 585 A ASP 586 n 78 ASP 586 A SER 587 n 79 SER 587 A VAL 588 n 80 VAL 588 A GLU 589 n 81 GLU 589 A TRP 590 n 82 TRP 590 A GLU 591 n 83 GLU 591 A SER 592 n 84 SER 592 A ASP 593 n 85 ASP 593 A PRO 594 n 86 PRO 594 A ASN 595 n 87 ASN 595 A ARG 596 n 88 ARG 596 A GLU 597 n 89 GLU 597 A TYR 598 n 90 TYR 598 A THR 599 n 91 THR 599 A VAL 600 n 92 VAL 600 A PRO 601 n 93 PRO 601 A GLN 602 n 94 GLN 602 A ALA 603 n 95 ALA 603 A CYS 604 n 96 CYS 604 A GLY 605 n 97 GLY 605 A THR 606 n 98 THR 606 A SER 607 n 99 SER 607 A THR 608 n 100 THR 608 A ALA 609 n 101 ALA 609 A THR 610 n 102 THR 610 A VAL 611 n 103 VAL 611 A THR 612 n 104 THR 612 A ASP 613 n 105 ASP 613 A THR 614 n 106 THR 614 A TRP 615 n 107 TRP 615 A ARG 616 n 108 ARG 616 A author_defined_assembly 1 monomeric 4160 39 5820 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 A O ALA 609 A O ALA 101 A N THR 518 A N THR 10 A O VAL 517 A O VAL 9 A N VAL 567 A N VAL 59 A O TYR 564 A O TYR 56 A N SER 552 A N SER 44 A O ILE 549 A O ILE 41 A N LEU 533 A N LEU 25 A O VAL 534 A O VAL 26 A N LYS 578 A N LYS 70 A O ARG 581 A O ARG 73 A N GLU 589 A N GLU 81 1 B C1 GLC 2 WRONG HAND 1 B C1 GLC 5 WRONG HAND 1 C C1 GLC 6 WRONG HAND 1 C C1 GLC 7 WRONG HAND 1 A A C H ILE TYR 531 532 1.17 1 A A H HE3 ILE TRP 531 563 1.30 1 A A O HB2 GLY ASP 535 542 1.32 1 A A O O GLY LEU 535 540 1.33 1 A A C HB2 GLY ASP 535 542 1.36 1 A C HG2 O2 PRO GLC 561 1 1.48 1 B B O4 O6 GLC GLC 4 5 2.18 1 A ARG 581 0.262 SIDE CHAIN 1 A ARG 596 0.312 SIDE CHAIN 1 A ARG 616 0.136 SIDE CHAIN 1 -3.62 0.60 121.00 117.38 A A A CB CG CD1 TYR TYR TYR 556 556 556 N 1 -3.69 0.60 121.00 117.31 A A A CB CG CD1 TYR TYR TYR 564 564 564 N 1 A THR 510 -141.90 -62.74 1 A THR 511 176.06 -55.14 1 A ALA 523 -141.04 -133.03 1 A THR 524 177.76 102.88 1 A THR 526 -108.76 65.48 1 A ASP 542 65.75 -19.16 1 A GLU 544 -170.01 82.86 1 A THR 545 -46.65 -13.26 1 A SER 558 -75.92 -120.07 1 A ASP 560 176.20 54.60 1 A TRP 563 19.21 93.58 1 A VAL 565 174.15 154.80 1 A THR 566 -157.56 86.82 1 A VAL 567 -116.46 -166.73 1 A ALA 571 -162.46 -66.86 1 A GLU 573 -162.23 -143.41 1 A ASP 585 -98.77 -76.65 1 A ASP 586 -65.47 -90.14 1 A SER 587 -170.18 -129.60 1 A GLU 589 -154.06 74.12 1 A TRP 590 -51.07 86.26 1 A GLU 591 -62.94 87.86 1 A ASP 593 -90.06 -66.72 1 A GLU 597 -160.03 88.33 1 A ALA 603 -59.63 -172.21 1 A THR 606 -158.35 63.80 1 A ALA 609 -135.45 -147.50 1 A VAL 611 -160.06 78.72 model building X-PLOR refinement X-PLOR phasing X-PLOR GLUCOAMYLASE GLUCOAMYLASE, GRANULAR STARCH-BINDING DOMAIN COMPLEX WITH CYCLODEXTRIN, NMR, MINIMIZED AVERAGE STRUCTURE 1 Y N 2 N N 2 N N A THR 545 A THR 37 HELX_P A ASP 547 A ASP 39 5 1 3 disulf 2.020 A CYS 509 A SG CYS 1 1_555 A CYS 604 A SG CYS 96 1_555 covale 1.402 both B GLC 1 B O4 GLC 1_555 B GLC 2 B C1 GLC 1_555 covale 1.400 both B GLC 1 B C1 GLC 1_555 B GLC 7 B O4 GLC 1_555 covale 1.400 both B GLC 2 B O4 GLC 1_555 B GLC 3 B C1 GLC 1_555 covale 1.403 both B GLC 3 B O4 GLC 1_555 B GLC 4 B C1 GLC 1_555 covale 1.400 both B GLC 4 B O4 GLC 1_555 B GLC 5 B C1 GLC 1_555 covale 1.408 both B GLC 5 B O4 GLC 1_555 B GLC 6 B C1 GLC 1_555 covale 1.400 both B GLC 6 B O4 GLC 1_555 B GLC 7 B C1 GLC 1_555 covale 1.405 both C GLC 1 C O4 GLC 1_555 C GLC 2 C C1 GLC 1_555 covale 1.399 both C GLC 1 C C1 GLC 1_555 C GLC 7 C O4 GLC 1_555 covale 1.398 both C GLC 2 C O4 GLC 1_555 C GLC 3 C C1 GLC 1_555 covale 1.403 both C GLC 3 C O4 GLC 1_555 C GLC 4 C C1 GLC 1_555 covale 1.398 both C GLC 4 C O4 GLC 1_555 C GLC 5 C C1 GLC 1_555 covale 1.398 both C GLC 5 C O4 GLC 1_555 C GLC 6 C C1 GLC 1_555 covale 1.399 both C GLC 6 C O4 GLC 1_555 C GLC 7 C C1 GLC 1_555 HYDROLASE HYDROLASE, STARCH BINDING DOMAIN AMYG_ASPNG UNP 1 1 P04064 MSFRSLLALSGLVCTGLANVISKRATLDSWLSNEATVARTAILNNIGADGAWVSGADSGIVVASPSTDNPDYFYTWTRDS GLVLKTLVDLFRNGDTSLLSTIENYISAQAIVQGISNPSGDLSSGAGLGEPKFNVDETAYTGSWGRPQRDGPALRATAMI GFGQWLLDNGYTSTATDIVWPLVRNDLSYVAQYWNQTGYDLWEEVNGSSFFTIAVQHRALVEGSAFATAVGSSCSWCDSQ APEILCYLQSFWTGSFILANFDSSRSGKDANTLLGSIHTFDPEAACDDSTFQPCSPRALANHKEVVDSFRSIYTLNDGLS DSEAVAVGRYPEDTYYNGNPWFLCTLAAAEQLYDALYQWDKQGSLEVTDVSLDFFKALYSDAATGTYSSSSSTYSSIVDA VKTFADGFVSIVETHAASNGSMSEQYDKSDGEQLSARDLTWSYAALLTANNRRNSVVPASWGETSASSVPGTCAATSAIG TYSSVTVTSWPSIVATGGTTTTATPTGSGSVTSTSKTTATASKTSTSTSSTSCTTPTAVAVTFDLTATTTYGENIYLVGS ISQLGDWETSDGIALSADKYTSSDPLWYVTVTLPAGESFEYKFIRIESDDSVEWESDPNREYTVPQACGTSTATVTDTWR 533 640 1AC0 509 616 P04064 A 1 1 108 7 parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A SER 607 A SER 99 A TRP 615 A TRP 107 A THR 513 A THR 5 A ALA 523 A ALA 15 A PRO 561 A PRO 53 A ALA 571 A ALA 63 A ILE 549 A ILE 41 A SER 552 A SER 44 A ASN 530 A ASN 22 A SER 536 A SER 28 A GLU 573 A GLU 65 A ILE 582 A ILE 74 A GLU 589 A GLU 81 A GLU 591 A GLU 83 1 P 1