MolNFT v1 · #149310 · protein + DNA
Structure of ding in complex with ssdna and adpbef
6FWS · ATP-dependent DNA helicase ding: “Structure of ding in complex with ssdna and adpbef”. X-ray diffraction, 4 ligands (SF4, ADP, BEF), 15 pockets (best druggability 0.83). MolNFT v1 #149310 on GenesisL1: 3D structure, binding sites…
- PDB
- 6FWS
- Type
- protein + DNA
- Length
- 1,390 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent DNA helicase ding; DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'); DNA…
- UniProt
- A0A2H4TNL0
- Ligands
- SF4, ADP, BEF, MG
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent DNA helicase ding | protein | 686 | 53% helix, 14% strand | A0A2H4TNL0 |
| C | DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 11 | — | — |
| B | ATP-dependent DNA helicase ding | protein | 683 | 53% helix, 14% strand | A0A2H4TNL0 |
| D | DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 10 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- BEF · Beryllium trifluoride ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.83 | 0.87 | 75 | empty |
| 2 | 515 | 0.82 | 0.88 | 53 | empty |
| 3 | 1055 | 0.79 | 0.81 | 86 | empty |
| 4 | 239 | 0.75 | 0.89 | 39 | ADP, BEF, MG |
| 5 | 235 | 0.73 | 0.88 | 39 | ADP, BEF, MG |
Interfaces
3 interfaces between chains.
- A–C · 1276 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–D · 1221 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–B · 837 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6FWS · Structure of DinG in complex with ssDNA and ADPBeF · the same entry in another collection · chain B against B, TM-score 1.00
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 A0A2H4TNL0
- Elsewhere: RCSB PDB 6FWS · PDBe 6FWS · UniProt A0A2H4TNL0
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