MolNFT v1 · #138053 · protein
Crystal structure of the group II chaperonin from methanococcus maripaludis D386ADELTALID mutant in the open, ADP-bound state
5W74: “Crystal structure of the group II chaperonin from methanococcus maripaludis D386ADELTALID mutant in the open…”. X-ray diffraction, 2 ligands (ADP, MG), 20 pockets (best druggability 0.80). MolNFT v1 #138053 on GenesisL1: 3D…
- PDB
- 5W74
- Type
- protein
- Length
- 3,816 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperonin
- UniProt
- Q877G8
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.80
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 | 477 | 50% helix, 18% 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
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 | 405 | 0.80 | 0.88 | 60 | ADP, MG |
| 2 | 390 | 0.79 | 0.88 | 60 | ADP, MG |
| 3 | 414 | 0.79 | 0.88 | 66 | ADP, MG |
| 4 | 475 | 0.78 | 0.86 | 62 | ADP, MG |
| 5 | 399 | 0.78 | 0.87 | 62 | ADP, MG |
Interfaces
8 interfaces between chains.
- A–B · 1162 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1150 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1144 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1144 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1143 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5W74 · Crystal Structure of the Group II Chaperonin from Methanococcus Maripaludis D386ADeltaLid… · 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 5W74 · PDBe 5W74 · UniProt Q877G8
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