MolNFT v1 · #62498 · protein
A D-pathway mutation decouples the paracoccus denitrificans cytochrome C oxidase by altering the side chain orientation of a distant, conserved glutamate
3EHB · Cytochrome C oxidase subunit 1-beta: “A D-pathway mutation decouples the paracoccus denitrificans cytochrome C oxidase by altering the side chain…”. X-ray diffraction, 5 ligands (HEA, CU, MG), 13 pockets (best druggability 0.90).…
- PDB
- 3EHB
- 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; Fv fragment chain H…
- EC
- 1.9.3.1
- UniProt
- P98002, P08306
- Ligands
- HEA, CU, MG, CA, PER
- Pockets
- 13 · 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 | 71% helix, 3% strand | P98002 |
| B | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 252 | 36% helix, 26% strand | P08306 |
| C | Fv fragment chain H | protein | 118 | 3% helix, 52% strand | — |
| D | Fv fragment chain L | protein | 108 | 3% helix, 50% strand | — |
Ligands and binding sites
- HEA · Heme-A · ligand · 2 copies · chains A, B
- CU · Copper (II) ion · metal · 3 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- CA · Calcium ion · metal · chains A
- PER · Peroxide ion · ion · chains A
- LMT · Dodecyl-beta-D-maltoside · additive · 12 copies · chains A, B, D
- LDA · Lauryl dimethylamine-N-oxide · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.90 | 0.92 | 123 | HEA, LMT, PER |
| 2 | 59 | 0.72 | 0.98 | 24 | empty |
| 3 | 381 | 0.62 | 0.78 | 47 | empty |
| 4 | 158 | 0.52 | 0.79 | 24 | empty |
| 5 | 136 | 0.49 | 0.78 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3966 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 952 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 443 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 415 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3EHB · A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by… · the same entry in another collection · chain A against A, 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 3EHB · PDBe 3EHB · UniProt P98002 · UniProt P08306
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