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
- 3KFK
- Type
- protein
- Length
- 1,945 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperonin
- UniProt
- Q877G8
- Ligands
- AGS
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Chaperonin | protein | 487 | 47% helix, 15% strand | Q877G8 |
| D | Chaperonin | protein | 484 | 46% helix, 16% strand | Q877G8 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.79 | 0.80 | 109 | AGS |
| 2 | 1057 | 0.77 | 0.79 | 109 | AGS |
| 3 | 1038 | 0.77 | 0.79 | 98 | AGS |
| 4 | 748 | 0.77 | 0.81 | 86 | AGS |
| 5 | 50 | 0.69 | 0.97 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1006 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 986 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 974 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3KFK · 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 3KFK · PDBe 3KFK · UniProt Q877G8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.