Research workbench
Atomic model of a pyrimidine dimer specific excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition
Analyse Atomic model of a pyrimidine dimer specific excision repair enzyme complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VAS
- Type
- protein + DNA
- Length
- 163 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3'); DNA…
- UniProt
- P04418
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3') | dna | 13 | — | — |
| C | DNA (5'-D(*TP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*GP*A)-3') | dna | 13 | — | — |
| A | Protein (T4 endonuclease V (E.C.3.1.25.1)) | protein | 137 | 51% helix, 1% strand | P04418 |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.58 | 0.90 | 14 | empty |
| 2 | 122 | 0.56 | 0.84 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–A · 772 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–A · 640 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 545 Ų buried · 43 hydrogen bonds · nucleic-nucleic
Compared structures
- 1VAS · Atomic model of a pyrimidine dimer specific excision repair enzyme complexed with a DNA… · 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 P04418
- Elsewhere: RCSB PDB 1VAS · PDBe 1VAS · UniProt P04418
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