Research workbench
X-ray structure of O-succinylbenzoate synthase complexed with N-succinyl methionine
Analyse X-ray structure of O-succinylbenzoate synthase complexed with N-succinyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SJC
- Type
- protein
- Length
- 1,470 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acylamino acid racemase
- UniProt
- Q44244
- Ligands
- SMG, MG
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | N-acylamino acid racemase | protein | 367 | 37% helix, 20% strand | Q44244 |
| B, D | N-acylamino acid racemase | protein | 368 | 37% helix, 24% strand | Q44244 |
Ligands and binding sites
- SMG · N-succinyl methionine · 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
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.87 | 0.88 | 118 | empty |
| 2 | 626 | 0.85 | 0.90 | 66 | empty |
| 3 | 85 | 0.74 | 0.97 | 25 | SMG |
| 4 | 78 | 0.74 | 0.97 | 23 | SMG |
| 5 | 254 | 0.72 | 0.87 | 54 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1249 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1225 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1051 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 146 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 125 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1SJC · x-ray structure of o-succinylbenzoate synthase complexed with N-succinyl methionine · 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 1SJC · PDBe 1SJC · UniProt Q44244
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