MolNFT v1 · #159200 · protein
Structure of tungstate bound human phospholipase D2 catalytic domain
6OHM: “Structure of tungstate bound human phospholipase D2 catalytic domain”. X-ray diffraction, 2 ligands (SO4, WO4), 13 pockets (best druggability 0.76). MolNFT v1 #159200 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OHM
- Type
- protein
- Length
- 1,158 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase D2
- EC
- 3.1.4.4
- UniProt
- O14939
- Ligands
- SO4, WO4
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase D2 (EC 3.1.4.4) | protein | 574 | 33% helix, 22% strand | O14939 |
| B | Phospholipase D2 (EC 3.1.4.4) | protein | 584 | 32% helix, 22% strand | O14939 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- WO4 · Tungstate(vi)ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.76 | 0.84 | 48 | WO4 |
| 2 | 455 | 0.73 | 0.82 | 45 | WO4 |
| 3 | 1068 | 0.71 | 0.75 | 70 | GOL |
| 4 | 380 | 0.61 | 0.77 | 29 | empty |
| 5 | 363 | 0.60 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 457 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
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 O14939
- Elsewhere: RCSB PDB 6OHM · PDBe 6OHM · UniProt O14939
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