Research workbench
Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase with a trapped plp-glutamate geminal diamine
Analyse Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase with a trapped… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R0T
- Type
- protein
- Length
- 772 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxamine 5-phosphate-dependent dehydrase
- UniProt
- Q9F118
- Ligands
- PGU
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyridoxamine 5-phosphate-dependent dehydrase | protein | 386 | 37% helix, 19% strand | Q9F118 |
Ligands and binding sites
- PGU · N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid · ligand · 2 copies · chains A, B
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 | 67 | 0.72 | 0.98 | 25 | empty |
| 2 | 349 | 0.68 | 0.82 | 50 | PGU |
| 3 | 384 | 0.68 | 0.81 | 50 | PGU |
| 4 | 266 | 0.57 | 0.77 | 32 | empty |
| 5 | 68 | 0.42 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2551 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2R0T · Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase with a trapped PLP-glutamate… · the same entry in another collection · chain B against B, 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 Q9F118
- Elsewhere: RCSB PDB 2R0T · PDBe 2R0T · UniProt Q9F118
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