Research workbench
N-acyl amino acid racemase from amycolatopsis sp. ts-1-60: Q26A M50I G291D F323Y mutant in complex with N-acetyl napthylalanine
Analyse N-acyl amino acid racemase from amycolatopsis sp. ts-1-60: Q26A M50I G291D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FJR
- Type
- protein
- Length
- 1,469 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
- 9 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-succinylbenzoate synthase (EC 4.2.1.113) | protein | 368 | 37% helix, 23% strand | Q44244 |
| B, C, D | O-succinylbenzoate synthase (EC 4.2.1.113) | protein | 367 | 36% 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
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.88 | 0.89 | 121 | empty |
| 2 | 1151 | 0.86 | 0.87 | 131 | empty |
| 3 | 195 | 0.73 | 0.90 | 30 | NPQ |
| 4 | 184 | 0.72 | 0.89 | 30 | NPQ |
| 5 | 201 | 0.72 | 0.88 | 29 | NPQ |
Interfaces
5 interfaces between chains.
- B–D · 1332 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1304 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1083 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 142 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 139 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5FJR · N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: Q26A M50I G291D F323Y mutant… · 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 5FJR · PDBe 5FJR · UniProt Q44244
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