MolNFT v1 · #106233 · protein
Crystal structure of DPY30 complexed with BRE2
4RT4 · Protein dpy-30 homolog: “Crystal structure of DPY30 complexed with BRE2”. X-ray diffraction, 2 pockets (best druggability 0.54). MolNFT v1 #106233 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4RT4
- Type
- protein
- Length
- 225 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein dpy-30 homolog; Peptide from compass component BRE2
- UniProt
- Q9C005, P43132
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein dpy-30 homolog | protein | 50 | 76% helix, 0% strand | Q9C005 |
| C, D | Protein dpy-30 homolog | protein | 52 | 79% helix, 0% strand | Q9C005 |
| E | Peptide from compass component BRE2 | protein | 21 | 86% helix, 0% strand | P43132 |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.54 | 0.77 | 21 | empty |
| 2 | 197 | 0.50 | 0.76 | 31 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1251 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1250 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 528 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 498 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 383 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4RT4 · Crystal structure of Dpy30 complexed with Bre2 · the same entry in another collection · chain E against E, TM-score 1.00
- Q9C005 · AlphaFold monomer V2.0 prediction for protein dpy-30 homolog (Q9C005) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P43132 · AlphaFold monomer V2.0 prediction for compass component BRE2 (P43132) · a predicted model of the same protein · chain E against A, TM-score 0.61
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 Q9C005
- Every structure of UniProt P43132
- Elsewhere: RCSB PDB 4RT4 · PDBe 4RT4 · UniProt Q9C005 · UniProt P43132
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