MolNFT v1 · #38104 · protein
Crystal structure of E COLI GDP-4-keto-6-deoxy-D-mannose-3-dehydratase complexed with plp-glutamate ketimine intermediate
2GMU · Putative pyridoxamine 5-phosphate-dependent dehydrase, wbdk: “Crystal structure of E COLI GDP-4-keto-6-deoxy-D-mannose-3-dehydratase complexed with plp-glutamate ketimine…”. X-ray diffraction, 2 ligands (PDG, MG), 5 pockets (best…
- PDB
- 2GMU
- Type
- protein
- Length
- 780 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative pyridoxamine 5-phosphate-dependent dehydrase, wbdk
- Ligands
- PDG, MG
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative pyridoxamine 5-phosphate-dependent dehydrase, wbdk | protein | 390 | 39% helix, 19% strand | — |
Ligands and binding sites
- PDG · N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-glutamic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.73 | 0.81 | 63 | PDG |
| 2 | 494 | 0.72 | 0.82 | 59 | PDG |
| 3 | 59 | 0.69 | 0.97 | 23 | empty |
| 4 | 240 | 0.55 | 0.77 | 29 | empty |
| 5 | 52 | 0.31 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2608 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2GMU · Crystal structure of E coli GDP-4-keto-6-deoxy-D-mannose-3-dehydratase complexed with… · the same entry in another collection · chain A 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
- Elsewhere: RCSB PDB 2GMU · PDBe 2GMU
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