Research workbench
Crystal structure for methylobacterium extorquens pqqcd (natural fusion)
Analyse Crystal structure for methylobacterium extorquens pqqcd (natural fusion) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VRD
- Type
- protein
- Length
- 815 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
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Bifunctional coenzyme pqq synthesis protein C/D (EC 1.3.3.11) | protein | 209 | 69% helix, 0% strand | Q49150 |
| A | Bifunctional coenzyme pqq synthesis protein C/D (EC 1.3.3.11) | protein | 208 | 73% helix, 0% strand | Q49150 |
| B | Bifunctional coenzyme pqq synthesis protein C/D (EC 1.3.3.11) | protein | 195 | 73% helix, 0% strand | Q49150 |
| C | Bifunctional coenzyme pqq synthesis protein C/D (EC 1.3.3.11) | protein | 203 | 71% helix, 0% strand | Q49150 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.75 | 0.78 | 102 | empty |
| 2 | 375 | 0.65 | 0.79 | 41 | empty |
| 3 | 302 | 0.61 | 0.79 | 37 | empty |
| 4 | 262 | 0.55 | 0.77 | 33 | empty |
| 5 | 317 | 0.51 | 0.73 | 32 | empty |
Interfaces
4 interfaces between chains.
- D–B · 949 Ų buried · 4 hydrogen bonds · protein-protein
- D–C · 714 Ų buried · 10 hydrogen bonds · protein-protein
- D–A · 111 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 10 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VRD · Crystal structure for Methylobacterium extorquens PqqCD (natural fusion) · the same entry in another collection · chain C against C, 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 0.99
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 Q49150
- Elsewhere: RCSB PDB 5VRD · PDBe 5VRD · UniProt Q49150
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