MolNFT v1 · #51461 · protein
Crystal structure of RAG2-phd finger in complex with H3R2ME2SK4ME2 peptide
2V88 · Vdj recombination-activating protein 2: “Crystal structure of RAG2-phd finger in complex with H3R2ME2SK4ME2 peptide”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.55). MolNFT v1 #51461 on GenesisL1: 3D structure…
- PDB
- 2V88
- Type
- protein
- Length
- 171 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vdj recombination-activating protein 2; H3R2ME2SK4ME3 peptide
- UniProt
- P21784, Q5TEC6
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vdj recombination-activating protein 2 | protein | 78 | 14% helix, 12% strand | P21784 |
| D | H3R2ME2SK4ME3 peptide | protein | 8 | 0% helix, 25% strand | Q5TEC6 |
| F | H3R2ME2SK4ME3 peptide | protein | 7 | 0% helix, 29% strand | Q5TEC6 |
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 | 220 | 0.55 | 0.78 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–D · 621 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 568 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 356 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 174 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 2V88 · Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me2 peptide · the same entry in another collection · chain A against A, 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 0.68
- Q5TEC6 · AlphaFold monomer V2.0 prediction for histone HIST2H3PS2 (Q5TEC6) · a predicted model of the same protein · chain D against A, TM-score 0.36
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 Q5TEC6
- Elsewhere: RCSB PDB 2V88 · PDBe 2V88 · UniProt P21784 · UniProt Q5TEC6
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