MolNFT v1 · #124218 · protein
MN2+/5NSA-bound 5-nitroanthranilate aminohydrolase
5K8O · 5-nitroanthranilic acid aminohydrolase: “MN2+/5NSA-bound 5-nitroanthranilate aminohydrolase”. X-ray diffraction, 2 ligands (6R7, MN), 20 pockets (best druggability 0.77). MolNFT v1 #124218 on GenesisL1: 3D structure, binding sites…
- PDB
- 5K8O
- Type
- protein
- Length
- 3,378 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-nitroanthranilic acid aminohydrolase
- EC
- 3.5.99.8
- UniProt
- D3WZ85
- Ligands
- 6R7, MN
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | 5-nitroanthranilic acid aminohydrolase (EC 3.5.99.8) | protein | 422 | 37% helix, 22% strand | D3WZ85 |
| B, D | 5-nitroanthranilic acid aminohydrolase (EC 3.5.99.8) | protein | 425 | 36% helix, 21% strand | D3WZ85 |
| C, E, F, H | 5-nitroanthranilic acid aminohydrolase (EC 3.5.99.8) | protein | 421 | 35% helix, 22% strand | D3WZ85 |
Ligands and binding sites
- 6R7 · 5-nitrosalicylic acid · ligand · 8 copies · chains A, H, B, E, C, D, F, G
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.77 | 0.80 | 126 | empty |
| 2 | 1200 | 0.76 | 0.79 | 145 | empty |
| 3 | 1108 | 0.76 | 0.79 | 129 | empty |
| 4 | 86 | 0.76 | 0.98 | 31 | empty |
| 5 | 73 | 0.74 | 0.98 | 34 | empty |
Interfaces
8 interfaces between chains.
- B–E · 3697 Ų buried · 51 hydrogen bonds · protein-protein
- F–G · 3685 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 3664 Ų buried · 50 hydrogen bonds · protein-protein
- A–H · 3646 Ų buried · 47 hydrogen bonds · protein-protein
- D–H · 1595 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5K8O · Mn2+/5NSA-bound 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 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 D3WZ85
- Elsewhere: RCSB PDB 5K8O · PDBe 5K8O · UniProt D3WZ85
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