MolNFT v1 · #29216 · protein
Crystal structure of the sixteen heme cytochrome from desulfovibrio gigas
1Z1N: “Crystal structure of the sixteen heme cytochrome from desulfovibrio gigas”. X-ray diffraction, 4 ligands (HEC, NAG, NAA), 8 pockets (best druggability 0.82). MolNFT v1 #29216 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1Z1N
- Type
- protein
- Length
- 516 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sixteen heme cytochrome
- UniProt
- Q8VUI3
- Ligands
- HEC, NAG, NAA, ZN
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Sixteen heme cytochrome | protein | 516 | 39% helix, 8% strand | Q8VUI3 |
Ligands and binding sites
- HEC · Heme C · ligand · 16 copies · chains X
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains X
- NAA · 2-acetamido-2-deoxy-beta-D-allopyranose · sugar
- ZN · Zinc ion · metal · 3 copies · chains X
- GOL · Glycerol · additive · 5 copies · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 648 | 0.82 | 0.86 | 77 | ZN, HEC |
| 2 | 264 | 0.77 | 0.90 | 48 | HEC |
| 3 | 232 | 0.75 | 0.89 | 45 | HEC, GOL |
| 4 | 150 | 0.70 | 0.89 | 32 | HEC |
| 5 | 130 | 0.69 | 0.90 | 28 | HEC |
Modifications
Observed in the structure: 30 cofactor, 1 glycan (heme c attachment, N-glycosylation).
Compared structures
- 1Z1N · Crystal Structure of the sixteen heme cytochrome from Desulfovibrio gigas · the same entry in another collection · chain X against X, 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 Q8VUI3
- Elsewhere: RCSB PDB 1Z1N · PDBe 1Z1N · UniProt Q8VUI3
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