Research workbench
Crystal structure of the DNA-binding domain of human xpa in complex with DNA
Analyse Crystal structure of the DNA-binding domain of human xpa 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
- 6LAE
- Type
- protein + DNA
- Length
- 254 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein complementing xp-a cells; DNA…
- UniProt
- P23025
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA repair protein complementing xp-a cells | protein | 116 | 41% helix, 13% strand | P23025 |
| C | DNA (5'-D(P*GP*CP*AP*TP*CP*TP*CP*GP*CP*CP*T)-3') | dna | 11 | — | — |
| D | DNA (5'-D(P*TP*GP*GP*CP*GP*AP*GP*AP*TP*GP*C)-3') | dna | 11 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.79 | 0.81 | 63 | empty |
| 2 | 56 | 0.27 | 0.73 | 13 | empty |
Interfaces
6 interfaces between chains.
- C–D · 461 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- A–D · 349 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–C · 323 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–D · 276 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–C · 232 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 6LAE · Crystal structure of the DNA-binding domain of human XPA in complex with DNA · the same entry in another collection · chain A against A, TM-score 1.00
- P23025 · AlphaFold monomer V2.0 prediction for DNA repair protein complementing xp-a cells (P23025) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P23025
- Elsewhere: RCSB PDB 6LAE · PDBe 6LAE · UniProt P23025
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.