MolNFT v1 · #191070 · protein
Crystal structure of human RECQL5 helicase apo form in complex with engineered nanobody (gluebody) G2*-006
7ZMQ · ATP-dependent DNA helicase Q5: “Crystal structure of human RECQL5 helicase apo form in complex with engineered nanobody (gluebody) G2*-006”. X-ray diffraction, 2 ligands (ZN, SO4), 8 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 7ZMQ
- Type
- protein
- Length
- 1,133 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase Q5; Gluebody G2*-006
- EC
- 3.6.4.12
- UniProt
- O94762
- Ligands
- ZN, SO4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 443 | 48% helix, 16% strand | O94762 |
| B | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 442 | 48% helix, 16% strand | O94762 |
| K, C | Gluebody G2*-006 | protein | 124 | 5% helix, 61% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.71 | 0.76 | 88 | empty |
| 2 | 707 | 0.66 | 0.75 | 78 | empty |
| 3 | 109 | 0.45 | 0.79 | 19 | empty |
| 4 | 78 | 0.44 | 0.80 | 16 | empty |
| 5 | 127 | 0.41 | 0.75 | 26 | SO4 |
Interfaces
3 interfaces between chains.
- A–K · 807 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 792 Ų buried · 13 hydrogen bonds · protein-protein
- K–C · 604 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7ZMQ · 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 B against A, TM-score 0.73
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 7ZMQ · PDBe 7ZMQ · UniProt O94762
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