Research workbench
Structure of spx domain of the yeast inorganic polyphophate polymerase VTC4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone MACROH2A1.1
Analyse Structure of spx domain of the yeast inorganic polyphophate polymerase VTC4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LNC
- Type
- protein
- Length
- 731 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar transporter chaperone 4,CORE histone macro-H2A.1
- UniProt
- P47075, O75367
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar transporter chaperone 4,CORE histone macro-H2A.1 | protein | 364 | 59% helix, 10% strand | P47075, O75367 |
| B | Vacuolar transporter chaperone 4,CORE histone macro-H2A.1 | protein | 367 | 59% helix, 10% strand | P47075, O75367 |
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.78 | 0.83 | 89 | empty |
| 2 | 308 | 0.70 | 0.84 | 54 | empty |
| 3 | 283 | 0.66 | 0.82 | 36 | empty |
| 4 | 326 | 0.63 | 0.79 | 47 | empty |
| 5 | 240 | 0.63 | 0.81 | 54 | empty |
Interfaces
1 interface between chains.
- A–B · 1218 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5LNC · Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized… · the same entry in another collection · chain A against A, TM-score 1.00
- O75367 · AlphaFold monomer V2.0 prediction for core histone macro-H2A.1 (O75367) · a predicted model of the same protein · chain B against A, TM-score 0.52
- P47075 · AlphaFold monomer V2.0 prediction for vacuolar transporter chaperone 4 (P47075) · a predicted model of the same protein · chain A against A, TM-score 0.49
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 P47075
- Every structure of UniProt O75367
- Elsewhere: RCSB PDB 5LNC · PDBe 5LNC · UniProt P47075 · UniProt O75367
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