MolNFT v1 · #125516 · protein
Crystal structure of human RECQL5 helicase in complex with ADP/MG (tricilinc form).
5LB5 · ATP-dependent DNA helicase Q5: “Crystal structure of human RECQL5 helicase in complex with ADP/MG (tricilinc form).”. X-ray diffraction, 3 ligands (ADP, ZN, MG), 20 pockets (best druggability 0.71). MolNFT v1 #125516 on GenesisL1…
- PDB
- 5LB5
- Type
- protein
- Length
- 1,723 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase Q5
- EC
- 3.6.4.12
- UniProt
- O94762
- Ligands
- ADP, ZN, MG
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 430 | 48% helix, 15% strand | O94762 |
| B | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 433 | 48% helix, 15% strand | O94762 |
| C | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 426 | 48% helix, 15% strand | O94762 |
| D | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 434 | 48% helix, 15% strand | O94762 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B, 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 | 768 | 0.71 | 0.77 | 65 | empty |
| 2 | 618 | 0.65 | 0.75 | 75 | DMS, MG, ADP |
| 3 | 92 | 0.57 | 0.86 | 16 | DMS |
| 4 | 383 | 0.56 | 0.74 | 45 | empty |
| 5 | 340 | 0.55 | 0.74 | 44 | empty |
Interfaces
4 interfaces between chains.
- C–D · 784 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 263 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 137 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 80 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5LB5 · Crystal structure of human RECQL5 helicase in complex with ADP/Mg (tricilinc form). · 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 A against A, TM-score 0.75
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 5LB5 · PDBe 5LB5 · UniProt O94762
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