Research workbench
Outward-facing pglk with atpgammas bound
Analyse Outward-facing pglk with atpgammas bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HRC
- Type
- protein
- Length
- 2,256 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wlab protein
- UniProt
- O86150
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 63% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Wlab protein | protein | 564 | 63% helix, 5% strand | O86150 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.89 | 0.93 | 92 | AGS |
| 2 | 1161 | 0.88 | 0.89 | 116 | AGS, MG |
| 3 | 992 | 0.87 | 0.87 | 132 | empty |
| 4 | 1086 | 0.86 | 0.87 | 120 | empty |
| 5 | 90 | 0.74 | 0.96 | 22 | empty |
Interfaces
5 interfaces between chains.
- C–D · 6632 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 6630 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 451 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 338 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 255 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6HRC · Outward-facing PglK with ATPgammaS bound · 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 O86150
- Elsewhere: RCSB PDB 6HRC · PDBe 6HRC · UniProt O86150
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