MolNFT v1 · #137528 · protein
Crystal structure for methylobacterium extorquens pqqc (truncation of natural CD fusion)
5VRC · Bifunctional coenzyme pqq synthesis protein C/D: “Crystal structure for methylobacterium extorquens pqqc (truncation of natural CD fusion)”. X-ray diffraction, 14 pockets (best druggability 0.71). MolNFT v1 #137528 on GenesisL1: 3D…
- PDB
- 5VRC
- Type
- protein
- Length
- 904 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional coenzyme pqq synthesis protein C/D
- EC
- 1.3.3.11
- UniProt
- Q49150
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional coenzyme pqq synthesis protein C/D (EC 1.3.3.11) | protein | 227 | 70% helix, 0% strand | Q49150 |
| B | Bifunctional coenzyme pqq synthesis protein C/D (EC 1.3.3.11) | protein | 228 | 70% helix, 0% strand | Q49150 |
| C | Bifunctional coenzyme pqq synthesis protein C/D (EC 1.3.3.11) | protein | 226 | 70% helix, 1% strand | Q49150 |
| D | Bifunctional coenzyme pqq synthesis protein C/D (EC 1.3.3.11) | protein | 223 | 68% helix, 1% strand | Q49150 |
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.71 | 0.98 | 22 | empty |
| 2 | 57 | 0.71 | 0.97 | 21 | empty |
| 3 | 369 | 0.63 | 0.78 | 38 | empty |
| 4 | 226 | 0.62 | 0.82 | 31 | empty |
| 5 | 356 | 0.60 | 0.77 | 42 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1120 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1081 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 789 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 781 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5VRC · Crystal structure for Methylobacterium extorquens PqqC (truncation of natural CD fusion) · the same entry in another collection · chain D against D, TM-score 1.00
- Q49150 · AlphaFold monomer V2.0 prediction for bifunctional coenzyme pqq synthesis protein C/D… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q49150
- Elsewhere: RCSB PDB 5VRC · PDBe 5VRC · UniProt Q49150
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