Research workbench
Sr CA(2+)-ATPase in the HNE2 state complexed with the thapsigargin derivative dotg
Analyse Sr CA(2+)-ATPase in the HNE2 state complexed with the thapsigargin derivative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NAM
- Type
- protein
- Length
- 994 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERCA1A
- EC
- 3.6.3.8
- UniProt
- B6CAM1
- Ligands
- OTK, PTY, NA, MG
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERCA1A (EC 3.6.3.8) | protein | 994 | 47% helix, 15% strand | B6CAM1 |
Ligands and binding sites
- OTK · (3S,3aR,4S,6S,6aS,8R,9R,9aR,9bS)-6-(acetyloxy)-4-(butanoyloxy)-3,3a-dihydroxy-3,6,9-trimethyl-2-oxododecahydroazuleno[4,5-b]furan-8-yl (2Z)-2-methylbut-2-enoate · ligand · chains A
- PTY · Phosphatidylethanolamine · ligand · chains A
- NA · Sodium ion · metal · chains A
- MG · Magnesium ion · metal · chains A
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 | 1022 | 0.80 | 0.82 | 90 | MG |
| 2 | 804 | 0.77 | 0.80 | 61 | OTK, PTY |
| 3 | 507 | 0.75 | 0.83 | 47 | empty |
| 4 | 303 | 0.60 | 0.78 | 35 | empty |
| 5 | 220 | 0.51 | 0.76 | 24 | empty |
Compared structures
- 3NAM · SR Ca(2+)-ATPase in the HnE2 state complexed with the Thapsigargin derivative dOTg · 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 B6CAM1
- Elsewhere: RCSB PDB 3NAM · PDBe 3NAM · UniProt B6CAM1
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