MolNFT v1 · #137424 · protein
Crystal structure of dape in complex with the products (succinic acid and diaminopimelic acid)
5VO3 · Succinyl-diaminopimelate desuccinylase: “Crystal structure of dape in complex with the products (succinic acid and diaminopimelic acid)”. X-ray diffraction, 2 ligands (API, ZN), 1 pocket (best druggability 0.51). MolNFT v1 #137424…
- PDB
- 5VO3
- Type
- protein
- Length
- 380 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
- P44514
- Ligands
- API, ZN
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) | protein | 380 | 34% helix, 26% strand | P44514 |
Ligands and binding sites
- API · 2,6-diaminopimelic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- SIN · Succinic acid · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.51 | 0.77 | 33 | SIN, API |
Compared structures
- 5VO3 · Crystal structure of DapE in complex with the products (succinic acid and diaminopimelic… · the same entry in another collection · chain A against A, TM-score 1.00
- P44514 · AlphaFold monomer V2.0 prediction for succinyl-diaminopimelate desuccinylase (P44514) · a predicted model of the same protein · chain A against A, TM-score 0.82
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 P44514
- Elsewhere: RCSB PDB 5VO3 · PDBe 5VO3 · UniProt P44514
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