Research workbench
Structure of caulobacter crescentus VAPBC1 bound to operator DNA
Analyse Structure of caulobacter crescentus VAPBC1 bound to operator DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L6L
- Type
- protein + DNA
- Length
- 856 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vapb family protein; Ribonuclease vapc; DNA (27-mer)
- EC
- 3.1.-.-
- UniProt
- Q9AC34, Q9AC35
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 7 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vapb family protein | protein | 65 | 18% helix, 42% strand | Q9AC34 |
| B, C, F, G | Ribonuclease vapc (EC 3.1.-.-) | protein | 127 | 54% helix, 13% strand | Q9AC35 |
| D | Vapb family protein | protein | 84 | 14% helix, 35% strand | Q9AC34 |
| E | Vapb family protein | protein | 64 | 16% helix, 42% strand | Q9AC34 |
| H | Vapb family protein | protein | 81 | 4% helix, 35% strand | Q9AC34 |
| M | DNA (27-mer) | dna | 27 | — | — |
| N | DNA (27-mer) | dna | 27 | — | — |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.68 | 0.80 | 40 | empty |
| 2 | 318 | 0.65 | 0.81 | 32 | empty |
| 3 | 240 | 0.48 | 0.74 | 25 | empty |
| 4 | 62 | 0.43 | 0.82 | 18 | empty |
| 5 | 59 | 0.41 | 0.81 | 15 | empty |
Interfaces
29 interfaces between chains.
- E–H · 2054 Ų buried · 51 hydrogen bonds · protein-protein
- A–D · 2018 Ų buried · 53 hydrogen bonds · protein-protein
- C–H · 1505 Ų buried · 21 hydrogen bonds · protein-protein
- D–G · 1452 Ų buried · 17 hydrogen bonds · protein-protein
- M–N · 1216 Ų buried · 104 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 5L6L · Structure of Caulobacter crescentus VapBC1 bound to operator DNA · 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 5L6L · PDBe 5L6L · UniProt Q9AC34 · UniProt Q9AC35
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