MolNFT v1 · #51459 · protein
Crystal structure of RAG2-phd finger in complex with H3R2ME2AK4ME3 peptide
2V86 · Vdj recombination-activating protein 2: “Crystal structure of RAG2-phd finger in complex with H3R2ME2AK4ME3 peptide”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.46). MolNFT v1 #51459 on GenesisL1: 3D structure…
- PDB
- 2V86
- Type
- protein
- Length
- 181 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vdj recombination-activating protein 2; H3R2ME2AK4ME3 peptide
- UniProt
- P21784, P84228
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vdj recombination-activating protein 2 | protein | 82 | 21% helix, 11% strand | P21784 |
| D | H3R2ME2AK4ME3 peptide | protein | 8 | 0% helix, 25% strand | P84228 |
| E | H3R2ME2AK4ME3 peptide | protein | 9 | 0% helix, 22% 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
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.46 | 0.78 | 24 | empty |
| 2 | 144 | 0.42 | 0.75 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–E · 707 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 685 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 404 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 194 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (methylation, nonstandard).
Compared structures
- 2V86 · Crystal structure of RAG2-PHD finger in complex with H3R2me2aK4me3 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
- P84228 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84228) · a predicted model of the same protein · chain D against A, TM-score 0.46
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 2V86 · PDBe 2V86 · UniProt P21784 · UniProt P84228
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