Research workbench
N-acyl amino acid racemase from amycolatopsis sp ts-1-60: G291D F323Y I293G mutant in complex with N-acetyl naphthylalanine
Analyse N-acyl amino acid racemase from amycolatopsis sp ts-1-60: G291D F323Y I293G… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FJP
- Type
- protein
- Length
- 1,470 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-succinylbenzoate synthase
- EC
- 4.2.1.113
- UniProt
- Q44244
- Ligands
- NPQ, MG
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | O-succinylbenzoate synthase (EC 4.2.1.113) | protein | 368 | 37% helix, 24% strand | Q44244 |
| C, D | O-succinylbenzoate synthase (EC 4.2.1.113) | protein | 367 | 37% helix, 23% strand | Q44244 |
Ligands and binding sites
- NPQ · N-acetyl naphthylalanine · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.86 | 0.87 | 121 | empty |
| 2 | 1126 | 0.86 | 0.87 | 121 | empty |
| 3 | 151 | 0.76 | 0.93 | 28 | NPQ |
| 4 | 163 | 0.74 | 0.91 | 35 | NPQ |
| 5 | 169 | 0.73 | 0.91 | 29 | NPQ |
Interfaces
5 interfaces between chains.
- A–C · 1291 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1282 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1078 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 133 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 133 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5FJP · N-acyl amino acid racemase from Amycolatopsis sp Ts-1-60: G291D F323Y I293G mutant in… · 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 5FJP · PDBe 5FJP · UniProt Q44244
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