Research workbench
Crystal strucutre of AF9 yeats domain in complex with a cyclopeptide inhibitor
Analyse Crystal strucutre of AF9 yeats domain in complex with a cyclopeptide inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L5Z
- Type
- protein
- Length
- 139 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein af-9; SC0-alo-ala-SC3-SC4-NH2
- UniProt
- P42568
- Ligands
- EDX, EE0, EE3, NH2
- Pockets
- 1 · best druggability 0.27
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein af-9 | protein | 137 | 10% helix, 50% strand | P42568 |
| C | SC0-alo-ala-SC3-SC4-NH2 | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- EDX · (2~{S})-6-carbamimidamido-2-(phenylmethoxycarbonylamino)hexanoic acid · ligand · chains A, C
- EE0 · (2~{R})-2-azanylpentanoic acid · ligand · chains A, C
- EE3 · (2~{S})-2-azanyl-6-(1,3-oxazol-5-ylcarbonylamino) hexanoic acid · ligand · chains A, C
- NH2 · Amino group · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.27 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–C · 138 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 6L5Z · Crystal strucutre of AF9 YEATS domain in complex with a cyclopeptide inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P42568 · AlphaFold monomer V2.0 prediction for protein af-9 (P42568) · a predicted model of the same protein · chain A against A, TM-score 0.99
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
- Elsewhere: RCSB PDB 6L5Z · PDBe 6L5Z · UniProt P42568
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.