Research workbench
Crystal structure of dape in complex with the products (succinic acid and diaminopimelic acid)
Analyse Crystal structure of dape in complex with the products (succinic acid and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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