Research workbench
Crystal structure of MUTT/NUDIX family hydrolase from rhodospirillum rubrum atcc 11170
Analyse Crystal structure of MUTT/NUDIX family hydrolase from rhodospirillum rubrum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DUP
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MUTT/NUDIX family protein
- UniProt
- Q2RXX6
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MUTT/NUDIX family protein | protein | 284 | 30% helix, 31% strand | Q2RXX6 |
| B | MUTT/NUDIX family protein | protein | 282 | 30% helix, 30% strand | Q2RXX6 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.82 | 0.83 | 110 | PO4, GOL |
| 2 | 79 | 0.63 | 0.91 | 22 | empty |
| 3 | 108 | 0.60 | 0.87 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1276 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3DUP · Crystal structure of mutt/nudix family hydrolase from rhodospirillum rubrum atcc 11170 · 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
- Every structure of UniProt Q2RXX6
- Elsewhere: RCSB PDB 3DUP · PDBe 3DUP · UniProt Q2RXX6
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