4WYG
Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis complexed with a fragment hit
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004015 | molecular_function | adenosylmethionine-8-amino-7-oxononanoate transaminase activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0008483 | molecular_function | transaminase activity |
| A | 0009102 | biological_process | biotin biosynthetic process |
| A | 0016740 | molecular_function | transferase activity |
| A | 0030170 | molecular_function | pyridoxal phosphate binding |
| B | 0004015 | molecular_function | adenosylmethionine-8-amino-7-oxononanoate transaminase activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0008483 | molecular_function | transaminase activity |
| B | 0009102 | biological_process | biotin biosynthetic process |
| B | 0016740 | molecular_function | transferase activity |
| B | 0030170 | molecular_function | pyridoxal phosphate binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 18 |
| Details | binding site for residue PLP A 501 |
| Chain | Residue |
| A | TRP65 |
| A | LYS283 |
| A | 3W1503 |
| A | HOH706 |
| A | HOH721 |
| A | HOH736 |
| A | HOH745 |
| B | GLY316 |
| B | PRO317 |
| B | THR318 |
| A | GLY124 |
| A | SER125 |
| A | TYR157 |
| A | HIS158 |
| A | GLU220 |
| A | ASP254 |
| A | ILE256 |
| A | ALA257 |
| site_id | AC2 |
| Number of Residues | 10 |
| Details | binding site for residue EPE A 502 |
| Chain | Residue |
| A | TYR25 |
| A | SER27 |
| A | GLU31 |
| A | TRP64 |
| A | ARG400 |
| A | 3W1503 |
| A | HOH740 |
| A | HOH807 |
| B | GLY93 |
| B | GLY94 |
| site_id | AC3 |
| Number of Residues | 13 |
| Details | binding site for residue 3W1 A 503 |
| Chain | Residue |
| A | TYR25 |
| A | TRP64 |
| A | TRP65 |
| A | TYR157 |
| A | ALA226 |
| A | ARG400 |
| A | PHE402 |
| A | PLP501 |
| A | EPE502 |
| A | HOH703 |
| A | HOH737 |
| B | GLY316 |
| B | THR318 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 504 |
| Chain | Residue |
| A | VAL222 |
| A | HIS232 |
| A | HOH878 |
| A | HOH996 |
| site_id | AC5 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 505 |
| Chain | Residue |
| A | ARG193 |
| A | ARG230 |
| A | PHE231 |
| A | ARG369 |
| A | HOH608 |
| A | HOH805 |
| A | HOH906 |
| A | HOH1024 |
| site_id | AC6 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 506 |
| Chain | Residue |
| A | ARG344 |
| A | ILE413 |
| A | CYS414 |
| A | THR415 |
| A | PRO416 |
| A | HOH827 |
| A | HOH974 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 507 |
| Chain | Residue |
| A | ALA113 |
| A | GLY273 |
| A | SER275 |
| A | HOH653 |
| A | HOH788 |
| site_id | AC8 |
| Number of Residues | 12 |
| Details | binding site for residue EPE B 502 |
| Chain | Residue |
| A | GLY93 |
| A | GLY94 |
| B | PRO24 |
| B | TYR25 |
| B | SER27 |
| B | GLU31 |
| B | TRP64 |
| B | LEU385 |
| B | ARG400 |
| B | 3W1503 |
| B | HOH724 |
| B | HOH795 |
| site_id | AC9 |
| Number of Residues | 13 |
| Details | binding site for residue 3W1 B 503 |
| Chain | Residue |
| A | GLY316 |
| A | THR318 |
| B | TYR25 |
| B | TRP64 |
| B | TRP65 |
| B | TYR157 |
| B | ALA226 |
| B | ARG400 |
| B | PHE402 |
| B | PLP501 |
| B | EPE502 |
| B | HOH672 |
| B | HOH712 |
| site_id | AD1 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 504 |
| Chain | Residue |
| B | TRP45 |
| B | GLU56 |
| site_id | AD2 |
| Number of Residues | 8 |
| Details | binding site for residue EDO B 505 |
| Chain | Residue |
| B | HOH630 |
| A | ALA211 |
| A | GLY212 |
| A | HOH616 |
| A | HOH624 |
| B | ARG154 |
| B | HIS171 |
| B | HOH611 |
| site_id | AD3 |
| Number of Residues | 11 |
| Details | binding site for residue 3W1 B 506 |
| Chain | Residue |
| B | ARG193 |
| B | VAL222 |
| B | PHE231 |
| B | HIS232 |
| B | ASP233 |
| B | PRO234 |
| B | HIS271 |
| B | HOH846 |
| B | HOH847 |
| B | HOH860 |
| B | HOH943 |
| site_id | AD4 |
| Number of Residues | 9 |
| Details | binding site for residue EDO B 507 |
| Chain | Residue |
| B | HIS23 |
| B | GLU31 |
| B | VAL33 |
| B | SER34 |
| B | PRO35 |
| B | EDO508 |
| B | HOH710 |
| B | HOH802 |
| B | HOH962 |
| site_id | AD5 |
| Number of Residues | 9 |
| Details | binding site for residue EDO B 508 |
| Chain | Residue |
| B | ASP17 |
| B | GLY18 |
| B | LEU21 |
| B | HIS23 |
| B | ILE28 |
| B | PRO35 |
| B | EDO507 |
| B | HOH869 |
| B | HOH961 |
| site_id | AD6 |
| Number of Residues | 8 |
| Details | binding site for residue EDO B 509 |
| Chain | Residue |
| A | LEU144 |
| B | ARG154 |
| B | GLN185 |
| B | VAL186 |
| B | PHE187 |
| B | HOH601 |
| B | HOH605 |
| B | HOH649 |
| site_id | AD7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 510 |
| Chain | Residue |
| A | HIS271 |
| A | ALA272 |
| B | ARG246 |
| B | EDO511 |
| B | HOH606 |
| site_id | AD8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 511 |
| Chain | Residue |
| B | ARG246 |
| B | TYR247 |
| B | EDO510 |
| B | HOH603 |
| site_id | AD9 |
| Number of Residues | 25 |
| Details | binding site for Di-peptide PLP B 501 and LYS B 283 |
| Chain | Residue |
| A | GLY316 |
| A | PRO317 |
| A | THR318 |
| A | PHE319 |
| B | TRP64 |
| B | TRP65 |
| B | GLY124 |
| B | SER125 |
| B | TYR157 |
| B | HIS158 |
| B | GLU220 |
| B | ASP254 |
| B | ILE256 |
| B | ALA257 |
| B | GLY282 |
| B | ALA284 |
| B | LEU285 |
| B | THR286 |
| B | 3W1503 |
| B | HOH698 |
| B | HOH702 |
| B | HOH716 |
| B | HOH758 |
| B | HOH762 |
| B | HOH861 |
Functional Information from PROSITE/UniProt
| site_id | PS00600 |
| Number of Residues | 38 |
| Details | AA_TRANSFER_CLASS_3 Aminotransferases class-III pyridoxal-phosphate attachment site. LIfDEIat.GFgRtGalfaadhagvsp....DIMcvGKaltGG |
| Chain | Residue | Details |
| A | LEU251-GLY288 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"20565114","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00834","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"20565114","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Site: {"description":"Participates in the substrate recognition with KAPA and in a stacking interaction with the adenine ring of SAM","evidences":[{"source":"PubMed","id":"20565114","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-(pyridoxal phosphate)lysine","evidences":[{"source":"PubMed","id":"20565114","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3BV0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3LV2","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
