MolNFT v1 · #149520 · protein
Crystal structure of the P97 D2 domain in a helical split-washer conformation
6G2Z · Transitional endoplasmic reticulum ATPase: “Crystal structure of the P97 D2 domain in a helical split-washer conformation”. X-ray diffraction, 3 ligands (ADP, EJW, NA), 4 pockets (best druggability 0.72). MolNFT v1 #149520 on…
- PDB
- 6G2Z
- Type
- protein
- Length
- 266 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transitional endoplasmic reticulum ATPase
- EC
- 3.6.4.6
- UniProt
- P55072
- Ligands
- ADP, EJW, NA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 266 | 53% helix, 12% strand | P55072 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- EJW · (3-phenyl-1,2-oxazol-5-yl)methylazanium · ligand · chains A
- NA · Sodium ion · metal · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.72 | 0.92 | 23 | MPD |
| 2 | 148 | 0.53 | 0.80 | 20 | MPD |
| 3 | 70 | 0.44 | 0.81 | 11 | MPD |
| 4 | 123 | 0.41 | 0.75 | 27 | ADP, NA |
Compared structures
- 6G2Z · Crystal structure of the p97 D2 domain in a helical split-washer conformation · 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
- Elsewhere: RCSB PDB 6G2Z · PDBe 6G2Z · UniProt P55072
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.