Research workbench
Crystal structure of RAG2-phd finger in complex with H3K4ME3 peptide
Analyse Crystal structure of RAG2-phd finger in complex with H3K4ME3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V83
- Type
- protein
- Length
- 239 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vdj recombination-activating protein 2; Histone H3
- UniProt
- P21784, Q5TEC6
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vdj recombination-activating protein 2 | protein | 71 | 18% helix, 11% strand | P21784 |
| B | Vdj recombination-activating protein 2 | protein | 79 | 19% helix, 11% strand | P21784 |
| C | Vdj recombination-activating protein 2 | protein | 71 | 14% helix, 11% strand | P21784 |
| D, E | Histone H3 | protein | 9 | 0% helix, 22% strand | Q5TEC6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.65 | 0.76 | 54 | empty |
| 2 | 271 | 0.53 | 0.76 | 35 | empty |
| 3 | 85 | 0.33 | 0.74 | 22 | empty |
Interfaces
8 interfaces between chains.
- A–D · 666 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 647 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 301 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 268 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 251 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 2V83 · Crystal structure of RAG2-PHD finger in complex with H3K4me3 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 0.72
- Q5TEC6 · AlphaFold monomer V2.0 prediction for histone HIST2H3PS2 (Q5TEC6) · a predicted model of the same protein · chain D against A, TM-score 0.35
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 2V83 · PDBe 2V83 · UniProt P21784 · UniProt Q5TEC6
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