MolNFT v1 · #21715 · protein
X-ray structure of O-succinylbenzoate synthase complexed with N-acetylmethionine
1SJA · N-acylamino acid racemase: “X-ray structure of O-succinylbenzoate synthase complexed with N-acetylmethionine”. X-ray diffraction, 2 ligands (AME, MG), 14 pockets (best druggability 0.86). MolNFT v1 #21715 on GenesisL1: 3D structure…
- PDB
- 1SJA
- Type
- protein
- Length
- 1,472 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acylamino acid racemase
- UniProt
- Q44244
- Ligands
- AME, MG
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | N-acylamino acid racemase | protein | 368 | 36% 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
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.86 | 0.88 | 124 | empty |
| 2 | 1119 | 0.86 | 0.87 | 112 | empty |
| 3 | 83 | 0.74 | 0.97 | 28 | AME |
| 4 | 72 | 0.72 | 0.97 | 24 | AME |
| 5 | 62 | 0.72 | 0.98 | 23 | AME |
Interfaces
5 interfaces between chains.
- A–B · 1256 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1204 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1085 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 130 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 122 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1SJA · X-ray structure of o-Succinylbenzoate Synthase complexed with N-acetylmethionine · 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 1SJA · PDBe 1SJA · UniProt Q44244
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