Research workbench
High resolution crystal structure of paracoccus denitrificans cytochrome C oxidase
Analyse High resolution crystal structure of paracoccus denitrificans cytochrome C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HB3
- Type
- protein
- Length
- 1,007 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase subunit 1-beta; Cytochrome C oxidase subunit 2; Antibody fv fragment
- EC
- 1.9.3.1
- UniProt
- P98002, P08306
- Ligands
- HEA, PEO, CU1, MN, CA
- Pockets
- 10 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C oxidase subunit 1-beta (EC 1.9.3.1) | protein | 529 | 70% helix, 2% strand | P98002 |
| B | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 252 | 36% helix, 26% strand | P08306 |
| C | Antibody fv fragment | protein | 118 | 3% helix, 48% strand | — |
| D | Antibody fv fragment | protein | 108 | 3% helix, 50% strand | — |
Ligands and binding sites
- HEA · Heme-A · ligand · 2 copies · chains A, B
- PEO · Hydrogen peroxide · ligand · chains A
- CU1 · Copper (I) ion · metal · 3 copies · chains A, B
- MN · Manganese (II) ion · metal · chains A, B
- CA · Calcium ion · metal · chains A
- LMT · Dodecyl-beta-D-maltoside · additive · 14 copies · chains A, B, D
- LDA · Lauryl dimethylamine-N-oxide · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.90 | 0.92 | 126 | HEA, LMT, PEO |
| 2 | 442 | 0.64 | 0.77 | 53 | empty |
| 3 | 157 | 0.51 | 0.79 | 24 | empty |
| 4 | 140 | 0.51 | 0.79 | 24 | LDA |
| 5 | 179 | 0.49 | 0.77 | 38 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3942 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 943 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 443 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 399 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3HB3 · High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase · the same entry in another collection · chain D against D, TM-score 1.00
- P98002 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 1-beta (P98002) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P08306 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 2 (P08306) · a predicted model of the same protein · chain B 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 P98002
- Every structure of UniProt P08306
- Elsewhere: RCSB PDB 3HB3 · PDBe 3HB3 · UniProt P98002 · UniProt P08306
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