Research workbench
Crystal structure of the catalytic domain of dape protein from V.CHOLEREA in the zn bound form
Analyse Crystal structure of the catalytic domain of dape protein from V.CHOLEREA in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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