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Crystal structure of the N-terminal 1-37 residues deleted mutant of geobacillus copper nitrite reductase
Analyse Crystal structure of the N-terminal 1-37 residues deleted mutant of geobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WIA
- Type
- protein
- Length
- 2,456 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrite reductase
- EC
- 1.7.2.1
- UniProt
- Q5L1X8
- Ligands
- CU
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Nitrite reductase (EC 1.7.2.1) | protein | 273 | 10% helix, 48% strand | Q5L1X8 |
| I | Nitrite reductase (EC 1.7.2.1) | protein | 272 | 10% helix, 49% strand | Q5L1X8 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 18 copies · chains A, B, C, D, E, F, G, H, I
- FMT · Formic acid · additive · 18 copies · chains A, B, C, D, E, F, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.81 | 0.92 | 38 | empty |
| 2 | 335 | 0.81 | 0.92 | 37 | empty |
| 3 | 269 | 0.81 | 0.92 | 45 | empty |
| 4 | 333 | 0.80 | 0.91 | 38 | empty |
| 5 | 257 | 0.80 | 0.92 | 45 | empty |
Interfaces
13 interfaces between chains.
- A–C · 1497 Ų buried · 32 hydrogen bonds · protein-protein
- H–I · 1481 Ų buried · 31 hydrogen bonds · protein-protein
- G–I · 1480 Ų buried · 33 hydrogen bonds · protein-protein
- D–E · 1476 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1470 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3WIA · Crystal structure of the N-terminal 1-37 residues deleted mutant of Geobacillus copper… · 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 Q5L1X8
- Elsewhere: RCSB PDB 3WIA · PDBe 3WIA · UniProt Q5L1X8
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