MolNFT v1 · #149519 · protein
Crystal structure of the P97 D2 domain in a helical split-washer conformation
6G2Y · Transitional endoplasmic reticulum ATPase: “Crystal structure of the P97 D2 domain in a helical split-washer conformation”. X-ray diffraction, 3 ligands (ADP, ELQ, NA), 4 pockets (best druggability 0.74). MolNFT v1 #149519 on…
- PDB
- 6G2Y
- 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, ELQ, NA
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 266 | 53% helix, 11% strand | P55072 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ELQ · [3,4-bis(fluoranyl)phenyl]-(4-methylpiperazin-1-yl)methanone · 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 | 129 | 0.74 | 0.93 | 26 | MPD |
| 2 | 156 | 0.55 | 0.80 | 19 | MPD |
| 3 | 133 | 0.47 | 0.78 | 29 | ADP, NA |
| 4 | 75 | 0.44 | 0.80 | 12 | MPD |
Compared structures
- 6G2Y · 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 6G2Y · PDBe 6G2Y · UniProt P55072
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