Research workbench
Crystal structure of RAG2-phd finger in complex with H3R2ME2SK4ME3 peptide
Analyse Crystal structure of RAG2-phd finger in complex with H3R2ME2SK4ME3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V87
- Type
- protein
- Length
- 178 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vdj recombination-activating protein 2; Histone H3.2
- UniProt
- P21784, P84228
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vdj recombination-activating protein 2 | protein | 77 | 14% helix, 12% strand | P21784 |
| B | Vdj recombination-activating protein 2 | protein | 79 | 19% helix, 10% strand | P21784 |
| D | Histone H3.2 | protein | 9 | 0% helix, 22% strand | P84228 |
| E | Histone H3.2 | protein | 13 | 0% helix, 15% strand | P84228 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.62 | 0.79 | 40 | empty |
Interfaces
4 interfaces between chains.
- B–E · 655 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 636 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 375 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 315 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 2V87 · Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide · the same entry in another collection · chain E against E, TM-score 1.00
- P21784 · AlphaFold monomer V2.0 prediction for V(D)J recombination-activating protein 2 (P21784) · a predicted model of the same protein · chain A against A, TM-score 0.69
- P84228 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84228) · a predicted model of the same protein · chain D against A, TM-score 0.38
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 P21784
- Every structure of UniProt P84228
- Elsewhere: RCSB PDB 2V87 · PDBe 2V87 · UniProt P21784 · UniProt P84228
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.