MolNFT v1 · #122224 · protein
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
5IIT · Vacuolar transporter chaperone 4,CORE histone macro-H2A.1: “Structure of spx domain of the yeast inorganic polyphophate polymerase VTC4 crystallized by carrier-driven…”. X-ray diffraction, 2 ligands (MG, SO4), 20 pockets (best…
- PDB
- 5IIT
- Type
- protein
- Length
- 1,424 residues
- Chains
- 4
- 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
- Ligands
- MG, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar transporter chaperone 4,CORE histone macro-H2A.1 | protein | 356 | 60% helix, 11% strand | P47075, O75367 |
| B | Vacuolar transporter chaperone 4,CORE histone macro-H2A.1 | protein | 356 | 60% helix, 11% strand | P47075, O75367 |
| C | Vacuolar transporter chaperone 4,CORE histone macro-H2A.1 | protein | 357 | 59% helix, 11% strand | P47075, O75367 |
| D | Vacuolar transporter chaperone 4,CORE histone macro-H2A.1 | protein | 355 | 59% helix, 12% strand | P47075, O75367 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.77 | 0.97 | 18 | empty |
| 2 | 832 | 0.76 | 0.80 | 58 | empty |
| 3 | 86 | 0.74 | 0.97 | 18 | empty |
| 4 | 685 | 0.73 | 0.79 | 69 | SO4 |
| 5 | 907 | 0.72 | 0.77 | 96 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3298 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 3213 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1293 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1265 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1148 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5IIT · Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized… · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.56
- 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 0.44
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 5IIT · PDBe 5IIT · UniProt P47075 · UniProt O75367
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