MolNFT v1 · #102547 · protein
Crystal structure of the catalytic domain of dape protein from V.CHOLEREA in the zn bound form
4OP4 · Succinyl-diaminopimelate desuccinylase: “Crystal structure of the catalytic domain of dape protein from V.CHOLEREA in the zn bound form”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.53). MolNFT v1 #102547 on…
- PDB
- 4OP4
- Type
- protein
- Length
- 528 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
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) | protein | 263 | 38% helix, 22% strand | Q9KQ52 |
| B | Succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) | protein | 265 | 38% helix, 22% strand | Q9KQ52 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- BU1 · 1,4-butanediol · additive · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.53 | 0.86 | 20 | BU1 |
| 2 | 81 | 0.52 | 0.85 | 19 | BU1 |
| 3 | 61 | 0.27 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 432 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4OP4 · Crystal structure of the catalytic domain of DapE protein from V.cholerea in the Zn bound… · 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 A 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 4OP4 · PDBe 4OP4 · UniProt Q9KQ52
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