Research workbench
Ccpa from G. sulfurreducens, S134P variant
Analyse Ccpa from G. sulfurreducens, S134P variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HQ9
- Type
- protein
- Length
- 618 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, OXL, CA
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C551 peroxidase (EC 1.11.1.5) | protein | 312 | 41% helix, 9% strand | Q749D0 |
| B | Cytochrome C551 peroxidase (EC 1.11.1.5) | protein | 306 | 39% helix, 10% strand | Q749D0 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B
- OXL · Oxalate ion · ligand · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- IMD · Imidazole · additive · 4 copies · chains A, B
- BU3 · (R,R)-2,3-butanediol · 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 | 1058 | 0.84 | 0.85 | 99 | HEM, IMD, OXL, BU3 |
| 2 | 1012 | 0.82 | 0.83 | 85 | HEM, CA, IMD, BU3 |
| 3 | 164 | 0.81 | 0.96 | 31 | OXL |
| 4 | 119 | 0.43 | 0.77 | 19 | OXL |
| 5 | 94 | 0.41 | 0.77 | 18 | OXL |
Interfaces
1 interface between chains.
- A–B · 1658 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme attachment).
Compared structures
- 3HQ9 · CcpA from G. sulfurreducens, S134P 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 3HQ9 · PDBe 3HQ9 · UniProt Q749D0
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