MolNFT v1 · #124213 · protein
Structure of caulobacter crescentus VAPBC1 (apo form)
5K8J · Vapb family protein: “Structure of caulobacter crescentus VAPBC1 (apo form)”. X-ray diffraction, 2 pockets (best druggability 0.53). MolNFT v1 #124213 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5K8J
- Type
- protein
- Length
- 402 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vapb family protein; Ribonuclease vapc
- EC
- 3.1.-.-
- UniProt
- Q9AC34, Q9AC35
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vapb family protein | protein | 80 | 13% helix, 33% strand | Q9AC34 |
| B, C | Ribonuclease vapc (EC 3.1.-.-) | protein | 127 | 60% helix, 13% strand | Q9AC35 |
| D | Vapb family protein | protein | 68 | 13% helix, 38% strand | Q9AC34 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.53 | 0.74 | 36 | empty |
| 2 | 84 | 0.32 | 0.74 | 23 | GOL |
Interfaces
5 interfaces between chains.
- A–D · 2029 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 1866 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1063 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 726 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 640 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 5K8J · Structure of Caulobacter crescentus VapBC1 (apo form) · the same entry in another collection · chain C against C, 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 Q9AC34
- Every structure of UniProt Q9AC35
- Elsewhere: RCSB PDB 5K8J · PDBe 5K8J · UniProt Q9AC34 · UniProt Q9AC35
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