Research workbench
Crystal structure of human RECQL5 helicase apo form in complex with engineered nanobody (gluebody) G1-001
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
- 7ZML
- Type
- protein
- Length
- 2,283 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase Q5; Gluebody G1-001 copies 1 and 2 in the asu
- EC
- 3.6.4.12
- UniProt
- O94762
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 441 | 47% helix, 15% strand | O94762 |
| D | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 440 | 50% helix, 15% strand | O94762 |
| K, G | Gluebody G1-001 copies 1 and 2 in the asu | protein | 131 | 7% helix, 60% strand | — |
| E | Gluebody G1-001 copies 1 and 2 in the asu | protein | 128 | 7% helix, 61% strand | — |
| F | Gluebody G1-001 copies 1 and 2 in the asu | protein | 130 | 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
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.74 | 0.83 | 62 | empty |
| 2 | 517 | 0.71 | 0.80 | 50 | empty |
| 3 | 311 | 0.70 | 0.83 | 45 | empty |
| 4 | 699 | 0.69 | 0.76 | 70 | empty |
| 5 | 683 | 0.67 | 0.75 | 78 | empty |
Interfaces
12 interfaces between chains.
- C–K · 780 Ų buried · 14 hydrogen bonds · protein-protein
- D–G · 766 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 749 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 747 Ų buried · 13 hydrogen bonds · protein-protein
- K–G · 698 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7ZML · Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody… · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.70
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 7ZML · PDBe 7ZML · UniProt O94762
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.