Research workbench
CA2+-ATPase from listeria monocytogenes with G4 insertion.
Analyse CA2+-ATPase from listeria monocytogenes with G4 insertion. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZHH
- Type
- protein
- Length
- 7,035 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calcium-transporting ATPase
- UniProt
- A0A1C7PY84
- Ligands
- PCW, BEF, CE1, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Calcium-transporting ATPase | protein | 883 | 51% helix, 16% strand | A0A1C7PY84 |
| E, F, H | Calcium-transporting ATPase | protein | 876 | 49% helix, 14% strand | A0A1C7PY84 |
| G | Calcium-transporting ATPase | protein | 875 | 50% helix, 15% strand | A0A1C7PY84 |
Ligands and binding sites
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 15 copies · chains A, B, C, D
- BEF · Beryllium trifluoride ion · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CE1 · O-dodecanyl octaethylene glycol · ligand · 7 copies · chains C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.81 | 0.84 | 68 | empty |
| 2 | 844 | 0.81 | 0.83 | 72 | empty |
| 3 | 881 | 0.80 | 0.83 | 73 | empty |
| 4 | 964 | 0.80 | 0.82 | 74 | PCW |
| 5 | 904 | 0.80 | 0.82 | 71 | empty |
Interfaces
10 interfaces between chains.
- F–G · 911 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 514 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 485 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 476 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 433 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6ZHH · Ca2+-ATPase from Listeria Monocytogenes with G4 insertion. · the same entry in another collection · chain C against C, 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 A0A1C7PY84
- Elsewhere: RCSB PDB 6ZHH · PDBe 6ZHH · UniProt A0A1C7PY84
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