Research workbench
Crystal structures of a group II chaperonin from methanococcus maripaludis
Analyse Crystal structures of a group II chaperonin from methanococcus maripaludis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KFE
- Type
- protein
- Length
- 3,896 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperonin
- UniProt
- Q877G8
- Ligands
- ADP, MG, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Chaperonin | protein | 487 | 45% helix, 17% strand | Q877G8 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
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 | 305 | 0.79 | 0.90 | 45 | MG, ADP, SO4 |
| 2 | 289 | 0.78 | 0.90 | 40 | MG, ADP, SO4 |
| 3 | 295 | 0.78 | 0.90 | 43 | MG, ADP, SO4 |
| 4 | 300 | 0.78 | 0.90 | 44 | MG, ADP, SO4 |
| 5 | 284 | 0.78 | 0.90 | 45 | MG, ADP, SO4 |
Interfaces
8 interfaces between chains.
- C–D · 2031 Ų buried · 33 hydrogen bonds · protein-protein
- D–E · 2030 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1940 Ų buried · 24 hydrogen bonds · protein-protein
- A–H · 1913 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1860 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3KFE · Crystal structures of a group II chaperonin from Methanococcus maripaludis · 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 Q877G8
- Elsewhere: RCSB PDB 3KFE · PDBe 3KFE · UniProt Q877G8
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