MolNFT v1 · #125521 · protein
Crystal structure of human RECQL5 helicase in complex with dspl FRAGMENT(1-cyclohexyl-3-(oxolan-2-YLMETHYL)UREA, sgc - diamond xchem I04-1 fragment screening.
5LBA · ATP-dependent DNA helicase Q5: “Crystal structure of human RECQL5 helicase in complex with dspl…”. X-ray diffraction, 4 ligands (ADP, 6SV, MG), 20 pockets (best druggability 0.66). MolNFT v1 #125521 on GenesisL1: 3D structure…
- PDB
- 5LBA
- Type
- protein
- Length
- 1,733 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, 6SV, MG, ZN
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 434 | 48% helix, 16% strand | O94762 |
| A | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 430 | 48% helix, 16% strand | O94762 |
| C | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 432 | 49% helix, 15% strand | O94762 |
| D | ATP-dependent DNA helicase Q5 (EC 3.6.4.12) | protein | 437 | 48% helix, 15% strand | O94762 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains B, A, C, D
- 6SV · 1-cyclohexyl-3-[[(2~{R})-oxolan-2-yl]methyl]urea · ligand · chains B
- MG · Magnesium ion · metal · 4 copies · chains B, A, C, D
- ZN · Zinc ion · metal · 4 copies · chains B, A, C, D
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains B, A, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.66 | 0.78 | 42 | empty |
| 2 | 508 | 0.64 | 0.76 | 64 | DMS |
| 3 | 100 | 0.61 | 0.87 | 19 | DMS |
| 4 | 283 | 0.61 | 0.80 | 41 | empty |
| 5 | 214 | 0.60 | 0.81 | 35 | 6SV |
Interfaces
4 interfaces between chains.
- C–D · 774 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 328 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 125 Ų buried · 1 hydrogen bond · protein-protein
- B–A · 93 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5LBA · Crystal structure of human RECQL5 helicase in complex with DSPL… · 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 0.75
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 5LBA · PDBe 5LBA · UniProt O94762
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