MolNFT v1 · #38033 · protein
Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap
2GKE: “Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap”. X-ray diffraction, 1 ligand (ZDP). MolNFT v1 #38033 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2GKE
- Type
- protein
- Length
- 274 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate epimerase
- EC
- 5.1.1.7
- UniProt
- P44859
- Ligands
- ZDP
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate epimerase (EC 5.1.1.7) | protein | 274 | 17% helix, 39% strand | P44859 |
Ligands and binding sites
- ZDP · (2S,6S)-2,6-diamino-2-methylheptanedioic acid · ligand · chains A
- ACY · Acetic acid · additive · 3 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2GKE · Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P44859 · AlphaFold monomer V2.0 prediction for diaminopimelate epimerase (P44859) · a predicted model of the same protein · chain A against A, TM-score 0.83
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 P44859
- Elsewhere: RCSB PDB 2GKE · PDBe 2GKE · UniProt P44859
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