MolNFT v1 · #8485 · protein
Sulfate respiration in desulfovibrio vulgaris hildenborough: structure of the 16-heme cytochrome C hmca at 2.5 a resolution and a view of its role in transmembrane electron transfer
1H29 · High-molecular-weight cytochrome C: “Sulfate respiration in desulfovibrio vulgaris hildenborough: structure of the 16-heme cytochrome C hmca at…”. X-ray diffraction, 1 ligand (HEC), 20 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 1H29
- Type
- protein
- Length
- 1,993 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High-molecular-weight cytochrome C
- UniProt
- P24092
- Ligands
- HEC
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High-molecular-weight cytochrome C | protein | 501 | 36% helix, 8% strand | P24092 |
| B | High-molecular-weight cytochrome C | protein | 499 | 38% helix, 8% strand | P24092 |
| C | High-molecular-weight cytochrome C | protein | 501 | 37% helix, 8% strand | P24092 |
| D | High-molecular-weight cytochrome C | protein | 492 | 35% helix, 7% strand | P24092 |
Ligands and binding sites
- HEC · Heme C · ligand · 64 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.89 | 0.90 | 154 | HEC |
| 2 | 751 | 0.87 | 0.90 | 122 | HEC |
| 3 | 977 | 0.86 | 0.87 | 111 | HEC |
| 4 | 352 | 0.83 | 0.93 | 61 | HEC |
| 5 | 386 | 0.81 | 0.90 | 59 | HEC |
Interfaces
2 interfaces between chains.
- A–C · 796 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 778 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 128 cofactor (heme c attachment).
Compared structures
- 1H29 · Sulfate respiration in Desulfovibrio vulgaris Hildenborough: Structure of the 16-heme… · the same entry in another collection · chain D against D, TM-score 1.00
- P24092 · AlphaFold monomer V2.0 prediction for high-molecular-weight cytochrome C (P24092) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P24092
- Elsewhere: RCSB PDB 1H29 · PDBe 1H29 · UniProt P24092
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.