Research workbench
Crystal structure of the P97 D2 domain in a helical split-washer conformation
Analyse Crystal structure of the P97 D2 domain in a helical split-washer conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G2W
- 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, AWD, NA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 266 | 50% helix, 12% strand | P55072 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- AWD · ~{N}-(4-fluorophenyl)-4-methyl-piperazine-1-carboxamide · 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 | 110 | 0.72 | 0.92 | 25 | MPD |
| 2 | 166 | 0.54 | 0.80 | 21 | MPD |
| 3 | 128 | 0.44 | 0.77 | 31 | ADP, NA |
| 4 | 71 | 0.43 | 0.81 | 13 | MPD |
Compared structures
- 6G2W · 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 6G2W · PDBe 6G2W · UniProt P55072
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