Research workbench
Crystal structure of the group II chaperonin from methanococcus maripaludis, cysteine-less mutant in the apo state
Analyse Crystal structure of the 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
- 5W79
- Type
- protein
- Length
- 4,120 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperonin
- UniProt
- Q877G8
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Chaperonin | protein | 515 | 50% helix, 18% strand | Q877G8 |
Ligands and binding sites
- 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 | 394 | 0.83 | 0.91 | 54 | SO4 |
| 2 | 346 | 0.81 | 0.90 | 51 | SO4 |
| 3 | 316 | 0.80 | 0.90 | 44 | SO4 |
| 4 | 576 | 0.80 | 0.85 | 75 | SO4 |
| 5 | 729 | 0.79 | 0.83 | 105 | SO4 |
Interfaces
16 interfaces between chains.
- D–E · 2923 Ų buried · 38 hydrogen bonds · protein-protein
- A–H · 2918 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2896 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2895 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 2831 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 5W79 · Crystal Structure of the 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 5W79 · PDBe 5W79 · UniProt Q877G8
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