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Crystal structure of diaminopimelate epimerase from arabidopsis thaliana in complex with ll-azidap
Analyse Crystal structure of diaminopimelate epimerase from arabidopsis thaliana in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EJX
- Type
- protein
- Length
- 1,751 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
- ZDP
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Diaminopimelate epimerase, chloroplastic (EC 5.1.1.7) | protein | 287 | 17% helix, 39% strand | Q9LFG2 |
| B | Diaminopimelate epimerase, chloroplastic (EC 5.1.1.7) | protein | 288 | 17% helix, 40% strand | Q9LFG2 |
| D, F | Diaminopimelate epimerase, chloroplastic (EC 5.1.1.7) | protein | 301 | 19% helix, 38% strand | Q9LFG2 |
Ligands and binding sites
- ZDP · (2S,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
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.69 | 0.79 | 52 | empty |
| 2 | 587 | 0.66 | 0.76 | 44 | empty |
| 3 | 255 | 0.57 | 0.78 | 31 | empty |
| 4 | 142 | 0.41 | 0.75 | 20 | empty |
| 5 | 101 | 0.35 | 0.74 | 18 | empty |
Interfaces
10 interfaces between chains.
- A–F · 969 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 932 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 877 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 452 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 448 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 3EJX · Crystal structure of diaminopimelate epimerase from 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 3EJX · PDBe 3EJX · UniProt Q9LFG2
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