MolNFT v1 · #124662 · protein
Crystal structure of HOPZ1A in complex with IP6
5KLP · ORF34: “Crystal structure of HOPZ1A in complex with IP6”. X-ray diffraction, 1 ligand (IHP), 7 pockets (best druggability 0.70). MolNFT v1 #124662 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KLP
- Type
- protein
- Length
- 934 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF34
- UniProt
- Q6VE93
- Ligands
- IHP
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ORF34 | protein | 309 | 51% helix, 12% strand | Q6VE93 |
| B | ORF34 | protein | 310 | 51% helix, 14% strand | Q6VE93 |
| C | ORF34 | protein | 315 | 50% helix, 13% strand | Q6VE93 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 3 copies · chains A, B, C
- CIT · Citric acid · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.70 | 0.77 | 66 | empty |
| 2 | 811 | 0.69 | 0.76 | 75 | IHP |
| 3 | 99 | 0.41 | 0.78 | 24 | IHP |
| 4 | 102 | 0.38 | 0.76 | 25 | IHP |
| 5 | 50 | 0.36 | 0.80 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 405 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 327 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 5KLP · Crystal structure of HopZ1a in complex with IP6 · the same entry in another collection · chain A against A, TM-score 1.00
- Q6VE93 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein acetyltransferase HOPZ1A… · a predicted model of the same protein · chain B against A, TM-score 1.00
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 Q6VE93
- Elsewhere: RCSB PDB 5KLP · PDBe 5KLP · UniProt Q6VE93
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