Research workbench
Crystal structure of full-length kluyveromyces lactis KAP123 with histone H3 1-28
Analyse Crystal structure of full-length kluyveromyces lactis KAP123 with histone H3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VE8
- Type
- protein
- Length
- 2,078 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KAP123; Histone H3
- UniProt
- Q6CMF0, P61831
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | KAP123 | protein | 1025 | 77% helix, 0% strand | Q6CMF0 |
| B | KAP123 | protein | 1030 | 78% helix, 0% strand | Q6CMF0 |
| C | Histone H3 | protein | 11 | 0% helix, 0% strand | P61831 |
| E | Histone H3 | protein | 12 | 0% helix, 0% strand | P61831 |
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.71 | 0.77 | 63 | empty |
| 2 | 642 | 0.69 | 0.77 | 63 | empty |
| 3 | 315 | 0.67 | 0.82 | 55 | empty |
| 4 | 304 | 0.66 | 0.82 | 42 | empty |
| 5 | 277 | 0.62 | 0.80 | 49 | empty |
Interfaces
3 interfaces between chains.
- B–E · 912 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 738 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 365 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 5VE8 · Crystal structure of full-length Kluyveromyces lactis Kap123 with histone H3 1-28 · the same entry in another collection · chain A against A, TM-score 1.00
- P61831 · AlphaFold monomer V2.0 prediction for histone H3 (P61831) · a predicted model of the same protein · chain E against A, TM-score 0.32
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 Q6CMF0
- Every structure of UniProt P61831
- Elsewhere: RCSB PDB 5VE8 · PDBe 5VE8 · UniProt Q6CMF0 · UniProt P61831
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