MolNFT v1 · #66434 · protein
Ccpa from G. sulfurreducens S134P/V135K variant
3HQ8 · Cytochrome C551 peroxidase: “Ccpa from G. sulfurreducens S134P/V135K variant”. X-ray diffraction, 2 ligands (HEM, CA), 5 pockets (best druggability 0.84). MolNFT v1 #66434 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3HQ8
- Type
- protein
- Length
- 628 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C551 peroxidase
- EC
- 1.11.1.5
- UniProt
- Q749D0
- Ligands
- HEM, CA
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C551 peroxidase (EC 1.11.1.5) | protein | 315 | 40% helix, 9% strand | Q749D0 |
| B | Cytochrome C551 peroxidase (EC 1.11.1.5) | protein | 313 | 38% helix, 10% strand | Q749D0 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.84 | 0.85 | 107 | HEM, CA, IMD |
| 2 | 1058 | 0.84 | 0.84 | 91 | HEM, CA, IMD |
| 3 | 165 | 0.80 | 0.96 | 32 | empty |
| 4 | 105 | 0.44 | 0.78 | 19 | empty |
| 5 | 115 | 0.42 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1726 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme attachment).
Compared structures
- 3HQ8 · CcpA from G. sulfurreducens S134P/V135K variant · 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 Q749D0
- Elsewhere: RCSB PDB 3HQ8 · PDBe 3HQ8 · UniProt Q749D0
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