Research workbench
P97 ND1-A232E in complex with vimp
Analyse P97 ND1-A232E in complex with vimp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KIY
- Type
- protein
- Length
- 487 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transitional endoplasmic reticulum ATPase; Selenoprotein S
- EC
- 3.6.4.6
- UniProt
- P55072, Q9BQE4
- Ligands
- ANP, MG
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 454 | 38% helix, 22% strand | P55072 |
| B | Selenoprotein S | protein | 33 | 94% helix, 0% strand | Q9BQE4 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.67 | 0.77 | 35 | empty |
| 2 | 302 | 0.57 | 0.77 | 36 | ANP |
| 3 | 115 | 0.46 | 0.78 | 21 | empty |
| 4 | 82 | 0.45 | 0.81 | 14 | empty |
| 5 | 100 | 0.41 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 740 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5KIY · p97 ND1-A232E in complex with VIMP · 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 P55072
- Every structure of UniProt Q9BQE4
- Elsewhere: RCSB PDB 5KIY · PDBe 5KIY · UniProt P55072 · UniProt Q9BQE4
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