Research workbench
Amycolatopsis sp. T-1-60 N-succinylamino acid RACEMASE/O- succinylbenzoate synthase R266Q mutant in complex with N- succinylphenylglycine
Analyse Amycolatopsis sp. T-1-60 N-succinylamino acid RACEMASE/O- succinylbenzoate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S8W
- Type
- protein
- Length
- 1,469 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-succinylamino acid RACEMASE/O-succinylbenzoate synthase
- EC
- 4.2.1.113
- UniProt
- Q44244
- Ligands
- 8JI, MG
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-succinylamino acid RACEMASE/O-succinylbenzoate synthase (EC 4.2.1.113) | protein | 367 | 38% helix, 24% strand | Q44244 |
| C | N-succinylamino acid RACEMASE/O-succinylbenzoate synthase (EC 4.2.1.113) | protein | 368 | 38% helix, 23% strand | Q44244 |
| D | N-succinylamino acid RACEMASE/O-succinylbenzoate synthase (EC 4.2.1.113) | protein | 367 | 37% helix, 23% strand | Q44244 |
Ligands and binding sites
- 8JI · N-succinyl-L-phenylglycine · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.87 | 0.88 | 122 | empty |
| 2 | 897 | 0.86 | 0.88 | 90 | empty |
| 3 | 105 | 0.77 | 0.97 | 32 | 8JI |
| 4 | 96 | 0.76 | 0.97 | 26 | 8JI |
| 5 | 100 | 0.76 | 0.97 | 26 | 8JI |
Interfaces
5 interfaces between chains.
- B–C · 1330 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1304 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1121 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 134 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 120 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7S8W · Amycolatopsis sp. T-1-60 N-succinylamino acid racemase/o-succinylbenzoate synthase R266Q… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q44244
- Elsewhere: RCSB PDB 7S8W · PDBe 7S8W · UniProt Q44244
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