Research workbench
Solution structure of the C-clamp domain from human HDBP1 in complex with DNA
Analyse Solution structure of the C-clamp domain from human HDBP1 in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DTA
- Type
- protein + DNA
- Length
- 55 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SLC2A4 regulator; DNA (5'-D(*TP*AP*TP*GP*CP*CP*GP*GP*GP*AP*C)-3'); DNA…
- UniProt
- Q9NR83
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.25
Structure
solution nmr · 3 distinct chains · 45% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SLC2A4 regulator | protein | 33 | 45% helix, 0% strand | Q9NR83 |
| B | DNA (5'-D(*TP*AP*TP*GP*CP*CP*GP*GP*GP*AP*C)-3') | dna | 11 | — | — |
| C | DNA (5'-D(*GP*TP*CP*CP*CP*GP*GP*CP*AP*TP*A)-3') | dna | 11 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.25 | 0.72 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–C · 502 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- A–B · 459 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 350 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 7DTA · Solution structure of the C-clamp domain from human HDBP1 in complex with DNA · the same entry in another collection · chain C against C, TM-score 1.00
- Q9NR83 · AlphaFold monomer V2.0 prediction for SLC2A4 regulator (Q9NR83) · a predicted model of the same protein · chain A against A, TM-score 0.72
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 Q9NR83
- Elsewhere: RCSB PDB 7DTA · PDBe 7DTA · UniProt Q9NR83
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.