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Crystal structure of the vibrio cholerae replicative helicase (dnab) with GDP-ALF4
Analyse Crystal structure of the vibrio cholerae replicative helicase (dnab) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T66
- Type
- protein
- Length
- 2,644 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicative DNA helicase
- EC
- 3.6.4.12
- UniProt
- A0A085R2T8
- Ligands
- GDP, ALF, MG
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Replicative DNA helicase (EC 3.6.4.12) | protein | 440 | 52% helix, 13% strand | A0A085R2T8 |
| B, D | Replicative DNA helicase (EC 3.6.4.12) | protein | 441 | 51% helix, 13% strand | A0A085R2T8 |
| F | Replicative DNA helicase (EC 3.6.4.12) | protein | 442 | 51% helix, 13% strand | A0A085R2T8 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- ALF · Tetrafluoroaluminate ion · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, 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 | 465 | 0.75 | 0.84 | 54 | GDP, MG, ALF |
| 2 | 507 | 0.75 | 0.83 | 58 | GDP, MG, ALF |
| 3 | 1136 | 0.74 | 0.77 | 80 | GDP, ALF |
| 4 | 483 | 0.74 | 0.83 | 52 | GDP, MG, ALF |
| 5 | 534 | 0.74 | 0.82 | 59 | GDP, MG, ALF |
Interfaces
9 interfaces between chains.
- A–B · 3603 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 3513 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 3448 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 2693 Ų buried · 33 hydrogen bonds · protein-protein
- A–F · 1957 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6T66 · Crystal structure of the Vibrio cholerae replicative helicase (DnaB) with GDP-AlF4 · the same entry in another collection · chain D against D, 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 A0A085R2T8
- Elsewhere: RCSB PDB 6T66 · PDBe 6T66 · UniProt A0A085R2T8
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