MolNFT v1 · #107339 · protein + DNA
Structure of human recq-like helicase in complex with an oligonucleotide
4U7D · ATP-dependent DNA helicase Q1: “Structure of human recq-like helicase in complex with an oligonucleotide”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.78). MolNFT v1 #107339 on GenesisL1: 3D structure, binding…
- PDB
- 4U7D
- Type
- protein + DNA
- Length
- 2,166 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase Q1; DNA oligonucleotide
- EC
- 3.6.4.12
- UniProt
- P46063
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-dependent DNA helicase Q1 (EC 3.6.4.12) | protein | 527 | 43% helix, 17% strand | P46063 |
| C, D | ATP-dependent DNA helicase Q1 (EC 3.6.4.12) | protein | 530 | 43% helix, 17% strand | P46063 |
| P | DNA oligonucleotide | dna | 17 | — | — |
| Q | DNA oligonucleotide | dna | 16 | — | — |
| R | DNA oligonucleotide | dna | 8 | — | — |
| S | DNA oligonucleotide | dna | 11 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 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 | 718 | 0.78 | 0.82 | 73 | empty |
| 2 | 1155 | 0.75 | 0.78 | 84 | empty |
| 3 | 672 | 0.73 | 0.80 | 60 | empty |
| 4 | 822 | 0.73 | 0.78 | 71 | empty |
| 5 | 777 | 0.70 | 0.77 | 46 | empty |
Interfaces
10 interfaces between chains.
- A–D · 1177 Ų buried · 17 hydrogen bonds · protein-protein
- B–P · 572 Ų buried · 10 hydrogen bonds · protein-nucleic
- P–Q · 561 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–Q · 524 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 459 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4U7D · Structure of human RECQ-like helicase in complex with an oligonucleotide · the same entry in another collection · chain S against S, 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 0.92
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 4U7D · PDBe 4U7D · UniProt P46063
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