Research workbench
Crystal structure of uronate dehydrogenase from agrobacterium tumefaciens complexed with NADH and product
Analyse Crystal structure of uronate dehydrogenase from agrobacterium tumefaciens… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RFV
- Type
- protein
- Length
- 795 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uronate dehydrogenase
- EC
- 1.1.1.203
- UniProt
- Q7CRQ0
- Ligands
- NAI, 15L, PO4
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Uronate dehydrogenase (EC 1.1.1.203) | protein | 265 | 40% helix, 18% strand | Q7CRQ0 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 3 copies · chains A, B, C
- 15L · D-galactaro-1,5-lactone · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.71 | 0.83 | 48 | empty |
| 2 | 362 | 0.63 | 0.78 | 41 | NAI, 15L |
| 3 | 340 | 0.63 | 0.79 | 45 | NAI, 15L |
| 4 | 351 | 0.63 | 0.79 | 44 | NAI, 15L |
| 5 | 286 | 0.56 | 0.77 | 43 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1462 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 558 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3RFV · Crystal structure of Uronate dehydrogenase from Agrobacterium tumefaciens complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7CRQ0 · AlphaFold monomer V2.0 prediction for uronate dehydrogenase (Q7CRQ0) · a predicted model of the same protein · 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
- Every structure of UniProt Q7CRQ0
- Elsewhere: RCSB PDB 3RFV · PDBe 3RFV · UniProt Q7CRQ0
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