Research workbench
Crystal structure of human RECQL5 helicase apo form in complex with engineered nanobody (gluebody) G2-001
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
- 7ZMM
- Type
- protein
- Length
- 2,277 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase Q5; Gluebody G2-001 copy 1 in the asu
- EC
- 3.6.4.12
- UniProt
- O94762
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, D | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 441 | 49% helix, 15% strand | O94762 |
| A | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 440 | 49% helix, 15% strand | O94762 |
| K | Gluebody G2-001 copy 1 in the asu | protein | 131 | 7% helix, 60% strand | — |
| E | Gluebody G2-001 copy 1 in the asu | protein | 130 | 5% helix, 60% strand | — |
| F | Gluebody G2-001 copy 1 in the asu | protein | 126 | 7% helix, 62% strand | — |
| G | Gluebody G2-001 copy 1 in the asu | protein | 127 | 5% helix, 61% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B, A, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.79 | 0.81 | 128 | empty |
| 2 | 944 | 0.75 | 0.78 | 87 | empty |
| 3 | 884 | 0.73 | 0.78 | 85 | empty |
| 4 | 665 | 0.67 | 0.76 | 63 | empty |
| 5 | 578 | 0.66 | 0.76 | 60 | empty |
Interfaces
12 interfaces between chains.
- A–K · 776 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 762 Ų buried · 13 hydrogen bonds · protein-protein
- D–G · 760 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 756 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 655 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7ZMM · 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 B 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 7ZMM · PDBe 7ZMM · UniProt O94762
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