Research workbench
Crystal structure of chromodomain of MPP8 in complex with inhibitor UNC3866
Analyse Crystal structure of chromodomain of MPP8 in complex with inhibitor UNC3866 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V2S
- Type
- protein
- Length
- 130 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M-phase phosphoprotein 8; UNC3866
- UniProt
- Q99549
- Ligands
- 5R0, UNX
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M-phase phosphoprotein 8 | protein | 60 | 35% helix, 40% strand | Q99549 |
| B | M-phase phosphoprotein 8 | protein | 60 | 43% helix, 40% strand | Q99549 |
| C, D | UNC3866 | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- 5R0 · 4-~{tert}-butylbenzoic acid · ligand · 2 copies · chains A, C, B, D
- UNX · Unknown atom or ion · ion · 19 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.51 | 0.81 | 20 | UNX |
Interfaces
4 interfaces between chains.
- B–D · 554 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 506 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 234 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 97 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent (nonstandard, covalent ligand).
Compared structures
- 6V2S · Crystal Structure of chromodomain of MPP8 in complex with inhibitor UNC3866 · the same entry in another collection · chain A against A, TM-score 1.00
- Q99549 · AlphaFold monomer V2.0 prediction for M-phase phosphoprotein 8 (Q99549) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 Q99549
- Elsewhere: RCSB PDB 6V2S · PDBe 6V2S · UniProt Q99549
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