Research workbench
Molecular basis of human xpc gene recognition and cleavage by engineered homing endonuclease heterodimers
Analyse Molecular basis of human xpc gene recognition and cleavage by engineered homing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VBJ
- Type
- protein + DNA
- Length
- 352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA endonuclease I-crei; 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP…
- EC
- 3.1.-.-
- UniProt
- P05725
- Ligands
- CA
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 152 | 51% helix, 20% strand | P05725 |
| B | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 152 | 55% helix, 21% strand | P05725 |
| C | 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP *TP*TP*GP*AP*AP*GP*GP*AP*TP*CP*CP*TP*AP*A)-3' | dna | 24 | — | — |
| E | 5'-D(*TP*TP*AP*GP*GP*AP*TP*CP*CP*TP *TP*CP*AP*AP*AP*AP*AP*AP*GP*GP*CP*AP*GP*A)-3' | dna | 24 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.78 | 0.93 | 43 | empty |
| 2 | 219 | 0.76 | 0.90 | 35 | empty |
| 3 | 59 | 0.48 | 0.85 | 20 | empty |
| 4 | 68 | 0.42 | 0.81 | 20 | empty |
| 5 | 55 | 0.41 | 0.81 | 13 | empty |
Interfaces
6 interfaces between chains.
- C–E · 1141 Ų buried · 89 hydrogen bonds · nucleic-nucleic
- A–C · 954 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–B · 940 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 891 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–C · 849 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 2VBJ · Molecular basis of human XPC gene recognition and cleavage by engineered homing… · the same entry in another collection · chain A against A, TM-score 1.00
- P05725 · AlphaFold monomer V2.0 prediction for DNA endonuclease I-crei (P05725) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P05725
- Elsewhere: RCSB PDB 2VBJ · PDBe 2VBJ · UniProt P05725
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