MolNFT v1 · #62611 · protein
Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor dl-azidap
3EKM · Diaminopimelate epimerase, chloroplastic: “Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible…”. X-ray diffraction, 1 ligand (ZDR), 13 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 3EKM
- Type
- protein
- Length
- 1,750 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate epimerase, chloroplastic
- EC
- 5.1.1.7
- UniProt
- Q9LFG2
- Ligands
- ZDR
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Diaminopimelate epimerase, chloroplastic (EC 5.1.1.7) | protein | 287 | 17% helix, 39% strand | Q9LFG2 |
| D, F | Diaminopimelate epimerase, chloroplastic (EC 5.1.1.7) | protein | 301 | 19% helix, 38% strand | Q9LFG2 |
Ligands and binding sites
- ZDR · (2R,6S)-2,6-diamino-2-methylheptanedioic acid · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 648 | 0.72 | 0.79 | 64 | empty |
| 2 | 418 | 0.69 | 0.81 | 45 | empty |
| 3 | 163 | 0.44 | 0.74 | 27 | empty |
| 4 | 149 | 0.42 | 0.75 | 22 | empty |
| 5 | 97 | 0.35 | 0.74 | 16 | empty |
Interfaces
10 interfaces between chains.
- A–F · 960 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 930 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 897 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 461 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 455 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 3EKM · Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9LFG2 · AlphaFold monomer V2.0 prediction for diaminopimelate epimerase, chloroplastic (Q9LFG2) · a predicted model of the same protein · chain E against A, TM-score 1.00
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 Q9LFG2
- Elsewhere: RCSB PDB 3EKM · PDBe 3EKM · UniProt Q9LFG2
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