Research workbench
High resolution crystal structure of an acylphosphatase protein cage
Analyse High resolution crystal structure of an acylphosphatase protein cage in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KRB
- Type
- protein
- Length
- 1,092 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acylphosphatase
- EC
- 3.6.1.7
- UniProt
- A5F8G9
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Acylphosphatase (EC 3.6.1.7) | protein | 91 | 26% helix, 38% strand | A5F8G9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 60 copies · chains A, B, K, F, J, C, I, H, D, E, G, L
- GOL · Glycerol · additive · 7 copies · chains A, C, F, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.80 | 0.84 | 107 | SO4 |
| 2 | 468 | 0.74 | 0.83 | 67 | SO4 |
| 3 | 286 | 0.73 | 0.87 | 41 | SO4 |
| 4 | 275 | 0.72 | 0.86 | 43 | SO4 |
| 5 | 279 | 0.71 | 0.85 | 42 | SO4 |
Interfaces
30 interfaces between chains.
- B–K · 401 Ų buried · 4 hydrogen bonds · protein-protein
- F–L · 397 Ų buried · 4 hydrogen bonds · protein-protein
- E–H · 396 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 395 Ų buried · 2 hydrogen bonds · protein-protein
- J–K · 387 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6KRB · High resolution crystal structure of an Acylphosphatase protein cage · the same entry in another collection · chain L against L, 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 A5F8G9
- Elsewhere: RCSB PDB 6KRB · PDBe 6KRB · UniProt A5F8G9
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