MolNFT v1 · #165581 · protein
Crystal structure of a LIPIN/PAH phosphatidic acid phosphatase
6TZY · Nuclear elongation and deformation protein: “Crystal structure of a LIPIN/PAH phosphatidic acid phosphatase”. X-ray diffraction, 1 ligand (CA), 13 pockets (best druggability 0.65). MolNFT v1 #165581 on GenesisL1: 3D structure…
- PDB
- 6TZY
- Type
- protein
- Length
- 1,063 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear elongation and deformation protein
- UniProt
- I7MFJ3
- Ligands
- CA
- Pockets
- 13 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear elongation and deformation protein | protein | 275 | 23% helix, 37% strand | I7MFJ3 |
| B | Nuclear elongation and deformation protein | protein | 265 | 24% helix, 34% strand | I7MFJ3 |
| C | Nuclear elongation and deformation protein | protein | 262 | 24% helix, 34% strand | I7MFJ3 |
| D | Nuclear elongation and deformation protein | protein | 261 | 25% helix, 32% strand | I7MFJ3 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.65 | 0.76 | 67 | empty |
| 2 | 534 | 0.63 | 0.76 | 57 | empty |
| 3 | 173 | 0.62 | 0.83 | 24 | empty |
| 4 | 163 | 0.53 | 0.80 | 23 | empty |
| 5 | 95 | 0.51 | 0.82 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–C · 734 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 300 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 234 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 126 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 56 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6TZY · Crystal Structure of a lipin/Pah Phosphatidic Acid Phosphatase · the same entry in another collection · chain A 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 I7MFJ3
- Elsewhere: RCSB PDB 6TZY · PDBe 6TZY · UniProt I7MFJ3
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