MolNFT v1 · #25438 · protein
Crystal structure of propionyl-CoA carboxylase, beta subunit (TM0716) from thermotoga maritima at 2.30 a resolution
1VRG: “Crystal structure of propionyl-CoA carboxylase, beta subunit (TM0716) from thermotoga maritima at 2.30 a…”. X-ray diffraction, 2 ligands (BCT, MG), 20 pockets (best druggability 0.83). MolNFT v1 #25438 on GenesisL1: 3D structure…
- PDB
- 1VRG
- Type
- protein
- Length
- 3,090 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Propionyl-CoA carboxylase, beta subunit
- EC
- 6.4.1.2
- UniProt
- Q9WZH5
- Ligands
- BCT, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Propionyl-CoA carboxylase, beta subunit (EC 6.4.1.2) | protein | 515 | 46% helix, 19% strand | Q9WZH5 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 10 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 3 copies · chains A, D, B, E, C, F
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 | 1107 | 0.83 | 0.84 | 97 | BCT |
| 2 | 1041 | 0.82 | 0.83 | 80 | empty |
| 3 | 808 | 0.80 | 0.83 | 72 | empty |
| 4 | 103 | 0.76 | 0.96 | 24 | empty |
| 5 | 90 | 0.76 | 0.97 | 24 | empty |
Interfaces
15 interfaces between chains.
- B–E · 4828 Ų buried · 62 hydrogen bonds · protein-protein
- A–D · 4813 Ų buried · 61 hydrogen bonds · protein-protein
- C–F · 4806 Ų buried · 60 hydrogen bonds · protein-protein
- D–F · 1326 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1322 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 78 modified (engineered).
Compared structures
- 1VRG · Crystal structure of propionyl-CoA carboxylase, beta subunit (TM0716) from THERMOTOGA… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9WZH5
- Elsewhere: RCSB PDB 1VRG · PDBe 1VRG · UniProt Q9WZH5
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