Research workbench
Structure of human recq-like helicase in complex with a DNA substrate
Analyse Structure of human recq-like helicase in complex with a DNA substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WWY
- Type
- protein + DNA
- Length
- 1,128 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase Q1; DNA oligo (27BP); 5'-D(*DA dg dc dg dt dc dg da dg da dt…
- EC
- 3.6.1.-
- UniProt
- P46063
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent DNA helicase Q1 (EC 3.6.1.-) | protein | 530 | 42% helix, 17% strand | P46063 |
| B | ATP-dependent DNA helicase Q1 (EC 3.6.1.-) | protein | 530 | 43% helix, 16% strand | P46063 |
| O | DNA oligo (27BP) | dna | 3 | — | — |
| P | 5'-D(*DA dg dc dg dt dc dg da dg da dt dc dcp)-3' | dna | 13 | — | — |
| Q | DNA oligo (27BP) | dna | 20 | — | — |
| R | DNA oligo (27BP) | dna | 2 | — | — |
| S | 5'-D(*DA dg dc dg dt dc dg da dg da dt dc dcp)-3' | dna | 12 | — | — |
| T | DNA oligo (27BP) | dna | 18 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.78 | 0.82 | 78 | SO4 |
| 2 | 1152 | 0.78 | 0.80 | 88 | SO4 |
| 3 | 75 | 0.73 | 0.97 | 17 | empty |
| 4 | 80 | 0.73 | 0.96 | 16 | empty |
| 5 | 849 | 0.73 | 0.78 | 46 | empty |
Interfaces
17 interfaces between chains.
- A–B · 1201 Ų buried · 12 hydrogen bonds · protein-protein
- A–Q · 741 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–T · 733 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–Q · 583 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- S–T · 558 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Compared structures
- 2WWY · Structure of human RECQ-like helicase in complex with a DNA substrate · the same entry in another collection · chain T against T, TM-score 1.00
- P46063 · AlphaFold monomer V2.0 prediction for ATP-dependent DNA helicase Q1 (P46063) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P46063
- Elsewhere: RCSB PDB 2WWY · PDBe 2WWY · UniProt P46063
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