MolNFT v1 · #108387 · protein
Complex structure of atrx add bound to H3K9ME3S10PH peptide
4W5A · Transcriptional regulator atrx: “Complex structure of atrx add bound to H3K9ME3S10PH peptide”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.75). MolNFT v1 #108387 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4W5A
- Type
- protein
- Length
- 402 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator atrx; Peptide from histone H3.3
- EC
- 3.6.4.12
- UniProt
- P46100, P84243
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator atrx (EC 3.6.4.12) | protein | 128 | 31% helix, 13% strand | P46100 |
| C, F | Peptide from histone H3.3 | protein | 11 | 0% helix, 36% strand | P84243 |
| B | Transcriptional regulator atrx (EC 3.6.4.12) | protein | 126 | 29% helix, 14% strand | P46100 |
| D | Peptide from histone H3.3 | protein | 12 | 0% helix, 33% strand | P84243 |
| E | Transcriptional regulator atrx (EC 3.6.4.12) | protein | 114 | 35% helix, 15% strand | P46100 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.75 | 0.82 | 62 | empty |
| 2 | 177 | 0.51 | 0.78 | 22 | empty |
| 3 | 94 | 0.40 | 0.76 | 15 | empty |
| 4 | 77 | 0.31 | 0.74 | 15 | empty |
| 5 | 51 | 0.30 | 0.76 | 14 | empty |
Interfaces
7 interfaces between chains.
- E–F · 744 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 736 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 701 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 644 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 623 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (methylation, phosphorylation).
Compared structures
- 4W5A · Complex structure of ATRX ADD bound to H3K9me3S10ph peptide · the same entry in another collection · chain E against E, TM-score 1.00
- P46100 · AlphaFold monomer V2.0 prediction for transcriptional regulator atrx (P46100) · a predicted model of the same protein · chain E against A, TM-score 0.96
- P84243 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84243) · a predicted model of the same protein · chain C 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 P46100
- Every structure of UniProt P84243
- Elsewhere: RCSB PDB 4W5A · PDBe 4W5A · UniProt P46100 · UniProt P84243
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