Research workbench
Crystal structure of succinyl-diaminopimelate desuccinylase from neisseria meningitidis MC58 in complex with the inhibitor captopril
Analyse Crystal structure of succinyl-diaminopimelate desuccinylase from neisseria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PQA
- Type
- protein
- Length
- 375 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinyl-diaminopimelate desuccinylase
- EC
- 3.5.1.18
- UniProt
- Q9JYL2
- Ligands
- X8Z, ZN, SO4
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) | protein | 375 | 31% helix, 28% strand | Q9JYL2 |
Ligands and binding sites
- X8Z · L-captopril · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.35 | 0.76 | 24 | X8Z |
Compared structures
- 4PQA · Crystal Structure of succinyl-diaminopimelate desuccinylase from Neisseria meningitidis… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9JYL2 · AlphaFold monomer V2.0 prediction for succinyl-diaminopimelate desuccinylase (Q9JYL2) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9JYL2
- Elsewhere: RCSB PDB 4PQA · PDBe 4PQA · UniProt Q9JYL2
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