MolNFT v1 · #191067 · protein
Crystal structure of human RECQL5 helicase apo form in complex with engineered nanobody (gluebody) G3-048
7ZMN · ATP-dependent DNA helicase Q5: “Crystal structure of human RECQL5 helicase apo form in complex with engineered nanobody (gluebody) G3-048”. X-ray diffraction, 2 ligands (ZN, SO4), 7 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 7ZMN
- Type
- protein
- Length
- 1,128 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase Q5; Gluebody G3-048
- EC
- 3.6.4.12
- UniProt
- O94762
- Ligands
- ZN, SO4
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 440 | 48% helix, 16% strand | O94762 |
| K, C | Gluebody G3-048 | protein | 124 | 2% helix, 60% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.68 | 0.76 | 70 | empty |
| 2 | 799 | 0.68 | 0.75 | 90 | empty |
| 3 | 138 | 0.44 | 0.76 | 27 | SO4 |
| 4 | 118 | 0.40 | 0.75 | 26 | SO4 |
| 5 | 72 | 0.36 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 796 Ų buried · 14 hydrogen bonds · protein-protein
- B–K · 779 Ų buried · 14 hydrogen bonds · protein-protein
- K–C · 623 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7ZMN · Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody… · the same entry in another collection · chain A against A, 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 0.72
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 7ZMN · PDBe 7ZMN · UniProt O94762
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