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Structure and atypical hydrolysis mechanism of the nudix hydrolase ORF153 (ymfb) from escherichia COLI
Analyse Structure and atypical hydrolysis mechanism of the nudix hydrolase ORF153… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NFX
- Type
- protein
- Length
- 1,209 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative nudix hydrolase ymfb
- UniProt
- G7RNP0
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F, G | Putative nudix hydrolase ymfb | protein | 153 | 21% helix, 37% strand | G7RNP0 |
| B | Putative nudix hydrolase ymfb | protein | 149 | 21% helix, 38% strand | G7RNP0 |
| D | Putative nudix hydrolase ymfb | protein | 150 | 21% helix, 37% strand | G7RNP0 |
| H | Putative nudix hydrolase ymfb | protein | 145 | 23% helix, 37% strand | G7RNP0 |
Pockets
10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.75 | 0.78 | 94 | empty |
| 2 | 886 | 0.74 | 0.78 | 92 | empty |
| 3 | 270 | 0.67 | 0.83 | 33 | empty |
| 4 | 168 | 0.54 | 0.80 | 30 | empty |
| 5 | 161 | 0.54 | 0.80 | 23 | empty |
Interfaces
11 interfaces between chains.
- E–F · 1693 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1673 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1666 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1643 Ų buried · 22 hydrogen bonds · protein-protein
- F–H · 446 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4NFX · Structure and atypical hydrolysis mechanism of the Nudix hydrolase Orf153 (YmfB) from… · 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 G7RNP0
- Elsewhere: RCSB PDB 4NFX · PDBe 4NFX · UniProt G7RNP0
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