MolNFT v1 · #102503 · protein
Crystal structure of the catalytic domain of dape protein from V.CHOLEREA
4ONW · Succinyl-diaminopimelate desuccinylase: “Crystal structure of the catalytic domain of dape protein from V.CHOLEREA”. X-ray diffraction, 5 pockets (best druggability 0.45). MolNFT v1 #102503 on GenesisL1: 3D structure, binding sites…
- PDB
- 4ONW
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinyl-diaminopimelate desuccinylase
- EC
- 3.5.1.18
- UniProt
- Q9KQ52
- Pockets
- 5 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) | protein | 265 | 39% helix, 22% strand | Q9KQ52 |
Ligands and binding sites
- BU1 · 1,4-butanediol · additive · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.45 | 0.84 | 17 | empty |
| 2 | 73 | 0.45 | 0.82 | 19 | ACT |
| 3 | 115 | 0.36 | 0.73 | 16 | empty |
| 4 | 70 | 0.28 | 0.72 | 15 | BU1 |
| 5 | 52 | 0.24 | 0.72 | 19 | BU1 |
Interfaces
1 interface between chains.
- A–B · 419 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4ONW · Crystal structure of the catalytic domain of DapE protein from V.cholerea · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KQ52 · AlphaFold monomer V2.0 prediction for succinyl-diaminopimelate desuccinylase (Q9KQ52) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9KQ52
- Elsewhere: RCSB PDB 4ONW · PDBe 4ONW · UniProt Q9KQ52
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