Research workbench
Structure of Caulobacter crescentus VapBC1 (VapB1deltaC:VapC1 form)
Analyse Structure of Caulobacter crescentus VapBC1 (VapB1deltaC:VapC1 form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L6M
- Type
- protein
- Length
- 1,173 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Caulobacter crescentus (strain ATCC 19089 / CB15)
- Molecule
- VapB family protein; Ribonuclease VapC
- EC
- 3.1.-.-
- UniProt
- Q9AC34, Q9AC35
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.9 · 6 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VapB family protein | protein | 66 | 15% helix, 39% strand | Q9AC34 |
| B, C, F, G, J, K | Ribonuclease VapC (EC 3.1.-.-) | protein | 127 | 59% helix, 13% strand | Q9AC35 |
| D | VapB family protein | protein | 71 | 18% helix, 37% strand | Q9AC34 |
| E | VapB family protein | protein | 66 | 5% helix, 42% strand | Q9AC34 |
| H, L | VapB family protein | protein | 70 | 19% helix, 40% strand | Q9AC34 |
| I | VapB family protein | protein | 68 | 19% helix, 43% strand | Q9AC34 |
Ligands and binding sites
- MLI · Malonate ion · additive · 3 copies · chains A, B, D, C, H, G
- GOL · Glycerol · additive · 2 copies · chains B, C, D, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.78 | 0.82 | 75 | empty |
| 2 | 305 | 0.69 | 0.84 | 41 | empty |
| 3 | 359 | 0.66 | 0.80 | 56 | MLI |
| 4 | 296 | 0.62 | 0.80 | 45 | MLI |
| 5 | 56 | 0.61 | 0.91 | 15 | empty |
Interfaces
30 interfaces between chains.
- E–H · 2081 Ų buried · 46 hydrogen bonds · protein-protein
- I–L · 1969 Ų buried · 55 hydrogen bonds · protein-protein
- A–D · 1848 Ų buried · 47 hydrogen bonds · protein-protein
- I–J · 1405 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1353 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5L6M · Structure of caulobacter crescentus VAPBC1 (VAPB1DELTAC:VAPC1 form) · 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 Q9AC34
- Every structure of UniProt Q9AC35
- Elsewhere: RCSB PDB 5L6M · PDBe 5L6M · UniProt Q9AC34 · UniProt Q9AC35
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