Research workbench
P97 ND1-L198W in complex with vimp
Analyse P97 ND1-L198W 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
- 5KIW
- Type
- protein
- Length
- 987 residues
- Chains
- 4
- 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
- 13 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 440 | 38% helix, 23% strand | P55072 |
| B | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 447 | 38% helix, 22% strand | P55072 |
| C | Selenoprotein S | protein | 38 | 89% helix, 0% strand | Q9BQE4 |
| D | Selenoprotein S | protein | 62 | 90% helix, 0% strand | Q9BQE4 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.64 | 0.75 | 39 | empty |
| 2 | 78 | 0.51 | 0.84 | 14 | empty |
| 3 | 305 | 0.49 | 0.73 | 40 | empty |
| 4 | 216 | 0.49 | 0.75 | 28 | ANP |
| 5 | 76 | 0.49 | 0.83 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–D · 831 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 813 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 153 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KIW · p97 ND1-L198W 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 5KIW · PDBe 5KIW · UniProt P55072 · UniProt Q9BQE4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.