Research workbench
N-acyl amino acid racemase from amycalotopsis sp. ts-1-60: G291D-F323Y mutant in complex with N-acetyl methionine
Analyse N-acyl amino acid racemase from amycalotopsis sp. ts-1-60: G291D-F323Y mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A6G
- Type
- protein
- Length
- 1,469 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acylamino acid racemase
- EC
- 4.2.1.113
- UniProt
- Q44244
- Ligands
- AME, MG
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acylamino acid racemase (EC 4.2.1.113) | protein | 368 | 38% helix, 23% strand | Q44244 |
| B, C, D | N-acylamino acid racemase (EC 4.2.1.113) | protein | 367 | 37% helix, 23% strand | Q44244 |
Ligands and binding sites
- AME · N-acetylmethionine · 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
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.87 | 0.90 | 105 | empty |
| 2 | 1077 | 0.87 | 0.88 | 117 | empty |
| 3 | 71 | 0.74 | 0.98 | 20 | AME |
| 4 | 67 | 0.71 | 0.96 | 20 | AME |
| 5 | 109 | 0.65 | 0.89 | 28 | AME |
Interfaces
5 interfaces between chains.
- A–C · 1275 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1262 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1102 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 142 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 107 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4A6G · N-acyl amino acid racemase from Amycalotopsis sp. Ts-1-60: G291D- F323Y mutant in complex… · the same entry in another collection · chain C against C, 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 4A6G · PDBe 4A6G · UniProt Q44244
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