Research workbench
Crystal structure of human RECQL5 helicase apo form in complex with engineered nanobody (gluebody) G5-006
Analyse Crystal structure of human RECQL5 helicase apo form in complex with engineered… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZMV
- Type
- protein
- Length
- 2,256 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase Q5; Gluebody G5-006
- EC
- 3.6.4.12
- UniProt
- O94762
- Ligands
- ZN, SO4
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 440 | 49% helix, 16% strand | O94762 |
| K, E, F, G | Gluebody G5-006 | protein | 124 | 5% helix, 60% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.69 | 0.76 | 87 | empty |
| 2 | 676 | 0.68 | 0.76 | 78 | empty |
| 3 | 684 | 0.66 | 0.75 | 73 | empty |
| 4 | 636 | 0.66 | 0.75 | 67 | empty |
| 5 | 219 | 0.50 | 0.76 | 32 | empty |
Interfaces
10 interfaces between chains.
- B–F · 795 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 794 Ų buried · 15 hydrogen bonds · protein-protein
- C–K · 793 Ų buried · 15 hydrogen bonds · protein-protein
- A–G · 792 Ų buried · 14 hydrogen bonds · protein-protein
- K–F · 567 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7ZMV · Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody… · the same entry in another collection · chain C against C, TM-score 1.00
- O94762 · AlphaFold monomer V2.0 prediction for ATP-dependent DNA helicase Q5 (O94762) · a predicted model of the same protein · chain A against A, TM-score 0.71
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 O94762
- Elsewhere: RCSB PDB 7ZMV · PDBe 7ZMV · UniProt O94762
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