MolNFT v1 · #152046 · protein
Cryo-EM informed directed evolution of nitrilase 4 leads to a change in quaternary structure.
6I5U · Bifunctional NITRILASE/NITRILE hydratase NIT4: “Cryo-EM informed directed evolution of nitrilase 4 leads to a change in quaternary structure.”. Electron microscopy, 18 pockets (best druggability 0.79). MolNFT v1 #152046 on…
- PDB
- 6I5U
- Type
- protein
- Length
- 1,734 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional NITRILASE/NITRILE hydratase NIT4
- EC
- 3.5.5.1, 3.5.5.4, 4.2.1.65
- UniProt
- P46011
- Pockets
- 18 · best druggability 0.79
Structure
electron microscopy · 1 distinct chain · 19% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, E, D, C, B, A | Bifunctional NITRILASE/NITRILE hydratase NIT4 (EC 3.5.5.1, 3.5.5.4, 4.2.1.65) | protein | 289 | 19% helix, 21% strand | P46011 |
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.79 | 0.82 | 91 | empty |
| 2 | 781 | 0.78 | 0.82 | 95 | empty |
| 3 | 123 | 0.61 | 0.86 | 23 | empty |
| 4 | 120 | 0.58 | 0.85 | 21 | empty |
| 5 | 115 | 0.58 | 0.85 | 21 | empty |
Interfaces
11 interfaces between chains.
- F–E · 2019 Ų buried · 25 hydrogen bonds · protein-protein
- D–C · 2016 Ų buried · 25 hydrogen bonds · protein-protein
- B–A · 2009 Ų buried · 25 hydrogen bonds · protein-protein
- D–B · 1215 Ų buried · 12 hydrogen bonds · protein-protein
- F–D · 1214 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6I5U · Cryo-EM informed directed evolution of Nitrilase 4 leads to a change in quaternary… · the same entry in another collection · chain D against D, TM-score 1.00
- P46011 · AlphaFold monomer V2.0 prediction for bifunctional NITRILASE/NITRILE hydratase NIT4… · a predicted model of the same protein · chain F against A, TM-score 0.96
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 P46011
- Elsewhere: RCSB PDB 6I5U · PDBe 6I5U · UniProt P46011
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