MolNFT v1 · #121040 · protein
AF9 yeats in complex with histone H3 crotonylation at K18
5HJD · Protein af-9: “AF9 yeats in complex with histone H3 crotonylation at K18”. X-ray diffraction, 2 ligands (CU, SO4), 12 pockets (best druggability 0.67). MolNFT v1 #121040 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HJD
- Type
- protein
- Length
- 1,152 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein af-9; Peptide of histone H3.1
- UniProt
- P42568, P68431
- Ligands
- CU, SO4
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, K, Q, T | Protein af-9 | protein | 138 | 9% helix, 53% strand | P42568 |
| N | Protein af-9 | protein | 137 | 11% helix, 52% strand | P42568 |
| L, M, B, D | Peptide of histone H3.1 | protein | 7 | 0% helix, 14% strand | P68431 |
| F, H, I | Peptide of histone H3.1 | protein | 5 | 0% helix, 20% strand | P68431 |
| J | Peptide of histone H3.1 | protein | 6 | 0% helix, 17% strand | P68431 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 4 copies · chains A, C, E, K, T
- SO4 · Sulfate ion · ion · 14 copies · chains A, C, E, G, K, N, Q, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.67 | 0.76 | 69 | SO4 |
| 2 | 608 | 0.67 | 0.76 | 71 | SO4 |
| 3 | 281 | 0.56 | 0.77 | 39 | SO4 |
| 4 | 341 | 0.55 | 0.75 | 46 | empty |
| 5 | 286 | 0.55 | 0.75 | 32 | CU |
Interfaces
17 interfaces between chains.
- A–C · 848 Ų buried · 21 hydrogen bonds · protein-protein
- Q–T · 846 Ų buried · 17 hydrogen bonds · protein-protein
- K–N · 778 Ų buried · 21 hydrogen bonds · protein-protein
- E–G · 770 Ų buried · 14 hydrogen bonds · protein-protein
- K–M · 519 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 8 modified (disulfide, nonstandard).
Compared structures
- 5HJD · AF9 YEATS in complex with histone H3 Crotonylation at K18 · the same entry in another collection · chain J against J, TM-score 1.00
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 P42568
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 5HJD · PDBe 5HJD · UniProt P42568 · UniProt P68431
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