Research workbench
Tvnir in complex with sulfite, middle dose data set
Analyse Tvnir in complex with sulfite, middle dose data set in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q5C
- Type
- protein
- Length
- 1,038 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eight-heme nitrite reductase
- UniProt
- Q5F2I3
- Ligands
- HEC, CA, SO3
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Eight-heme nitrite reductase | protein | 519 | 44% helix, 10% strand | Q5F2I3 |
Ligands and binding sites
- HEC · Heme C · ligand · 16 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO3 · Sulfite ion · ion · 5 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.88 | 0.90 | 108 | HEC, SO3 |
| 2 | 347 | 0.82 | 0.91 | 45 | HEC |
| 3 | 287 | 0.81 | 0.93 | 43 | HEC, SO3 |
| 4 | 232 | 0.80 | 0.93 | 40 | HEC |
| 5 | 215 | 0.79 | 0.93 | 45 | HEC |
Interfaces
1 interface between chains.
- A–B · 1270 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 cofactor (heme c attachment).
Compared structures
- 4Q5C · TvNiR in complex with sulfite, middle dose data set · 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 Q5F2I3
- Elsewhere: RCSB PDB 4Q5C · PDBe 4Q5C · UniProt Q5F2I3
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