MolNFT v1 · #51580 · protein + DNA
Molecular basis of human xpc gene recognition and cleavage by engineered homing endonuclease heterodimers
2VBO · DNA endonuclease I-crei: “Molecular basis of human xpc gene recognition and cleavage by engineered homing endonuclease heterodimers”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.73). MolNFT v1 #51580 on…
- PDB
- 2VBO
- Type
- protein + DNA
- Length
- 353 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
- 7 · best druggability 0.73
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 | 153 | 53% helix, 21% strand | P05725 |
| B | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 152 | 53% helix, 20% 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 · 4 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.73 | 0.89 | 41 | empty |
| 2 | 113 | 0.68 | 0.90 | 20 | empty |
| 3 | 85 | 0.62 | 0.90 | 20 | empty |
| 4 | 77 | 0.44 | 0.81 | 20 | empty |
| 5 | 61 | 0.42 | 0.82 | 21 | empty |
Interfaces
6 interfaces between chains.
- C–E · 1136 Ų buried · 99 hydrogen bonds · nucleic-nucleic
- A–B · 1008 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 934 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 865 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–E · 820 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 2VBO · 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 A against A, 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 P05725
- Elsewhere: RCSB PDB 2VBO · PDBe 2VBO · UniProt P05725
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