MolNFT v1 · #21718 · protein
X-ray structure of O-succinylbenzoate synthase complexed with N-succinyl phenylglycine
1SJD · N-acylamino acid racemase: “X-ray structure of O-succinylbenzoate synthase complexed with N-succinyl phenylglycine”. X-ray diffraction, 1 ligand (NPG), 12 pockets (best druggability 0.88). MolNFT v1 #21718 on GenesisL1: 3D…
- PDB
- 1SJD
- 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
- UniProt
- Q44244
- Ligands
- NPG
- Pockets
- 12 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | N-acylamino acid racemase | protein | 367 | 37% helix, 23% strand | Q44244 |
| B | N-acylamino acid racemase | protein | 368 | 37% helix, 24% strand | Q44244 |
Ligands and binding sites
- NPG · N-succinyl phenylglycine · ligand · 6 copies · chains A, B, C, D
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 | 1049 | 0.88 | 0.89 | 141 | empty |
| 2 | 804 | 0.86 | 0.89 | 76 | empty |
| 3 | 516 | 0.77 | 0.85 | 81 | empty |
| 4 | 90 | 0.76 | 0.98 | 25 | NPG |
| 5 | 92 | 0.76 | 0.97 | 28 | NPG |
Interfaces
5 interfaces between chains.
- A–B · 1230 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1213 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1062 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 151 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 131 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1SJD · x-ray structure of o-succinylbenzoate synthase complexed with n-succinyl phenylglycine · 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 1SJD · PDBe 1SJD · UniProt Q44244
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