Research workbench
Zn2+/Tetrahedral intermediate-bound R289A 5-nitroanthranilate aminohydrolase
Analyse Zn2+/Tetrahedral intermediate-bound R289A 5-nitroanthranilate aminohydrolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K8P
- Type
- protein
- Length
- 3,380 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Bradyrhizobium sp.
- Molecule
- 5-nitroanthranilic acid aminohydrolase
- EC
- 3.5.99.8
- UniProt
- D3WZ85
- Ligands
- 6R8, ZN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.2 · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G | 5-nitroanthranilic acid aminohydrolase (EC 3.5.99.8) | protein | 421 | 38% helix, 23% strand | D3WZ85 |
| C, H | 5-nitroanthranilic acid aminohydrolase (EC 3.5.99.8) | protein | 422 | 36% helix, 23% strand | D3WZ85 |
| D, F | 5-nitroanthranilic acid aminohydrolase (EC 3.5.99.8) | protein | 425 | 37% helix, 23% strand | D3WZ85 |
| E | 5-nitroanthranilic acid aminohydrolase (EC 3.5.99.8) | protein | 423 | 37% helix, 23% strand | D3WZ85 |
Ligands and binding sites
- 6R8 · (6~{R})-6-azanyl-3-nitro-6-oxidanyl-cyclohexa-1,3-diene-1-carboxylic acid · ligand · 6 copies · chains A, B, C, F, D, E, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 8 copies · chains A, C, B, G, D, H, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.76 | 0.89 | 45 | empty |
| 2 | 159 | 0.76 | 0.93 | 32 | 6R8 |
| 3 | 1170 | 0.76 | 0.78 | 151 | empty |
| 4 | 1017 | 0.76 | 0.78 | 123 | empty |
| 5 | 137 | 0.76 | 0.94 | 31 | 6R8 |
Interfaces
8 interfaces between chains.
- G–H · 3509 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 3502 Ų buried · 57 hydrogen bonds · protein-protein
- D–E · 3489 Ų buried · 53 hydrogen bonds · protein-protein
- C–F · 3443 Ų buried · 51 hydrogen bonds · protein-protein
- D–H · 1688 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5K8P · ZN2+/TETRAHEDRAL intermediate-bound R289A 5-nitroanthranilate aminohydrolase · the same entry in another collection · chain H against H, TM-score 1.00
- D3WZ85 · AlphaFold monomer V2.0 prediction for 5-nitroanthranilic acid aminohydrolase (D3WZ85) · a predicted model of the same protein · chain C 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 D3WZ85
- Elsewhere: RCSB PDB 5K8P · PDBe 5K8P · UniProt D3WZ85
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