MolNFT v1 · #77462 · protein
Crystal structure of uronate dehydrogenase from agrobacterium tumefaciens
3RFT: “Crystal structure of uronate dehydrogenase from agrobacterium tumefaciens”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.72). MolNFT v1 #77462 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3RFT
- Type
- protein
- Length
- 798 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
- SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Uronate dehydrogenase (EC 1.1.1.203) | protein | 266 | 39% helix, 18% strand | Q7CRQ0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 15 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 | 387 | 0.72 | 0.83 | 47 | empty |
| 2 | 371 | 0.63 | 0.78 | 45 | SO4 |
| 3 | 357 | 0.63 | 0.78 | 46 | SO4 |
| 4 | 358 | 0.62 | 0.78 | 45 | SO4 |
| 5 | 272 | 0.56 | 0.77 | 38 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1463 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 551 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3RFT · Crystal structure of uronate dehydrogenase from Agrobacterium tumefaciens · 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 0.99
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 3RFT · PDBe 3RFT · UniProt Q7CRQ0
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