MolNFT v1 · #103570 · protein
Crystal structure of the football-shaped groel-GROES2-(ADPBEFX)14 complex
4PKO · 60 kda chaperonin: “Crystal structure of the football-shaped groel-GROES2-(ADPBEFX)14 complex”. X-ray diffraction, 4 ligands (ADP, BEF, MG), 20 pockets (best druggability 0.85). MolNFT v1 #103570 on GenesisL1: 3D structure, binding…
- PDB
- 4PKO
- Type
- protein
- Length
- 8,687 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 60 kda chaperonin; 10 kda chaperonin
- UniProt
- Q548M1, Q7BGE6
- Ligands
- ADP, BEF, MG, K
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N | 60 kda chaperonin | protein | 524 | 50% helix, 16% strand | Q548M1 |
| O | 10 kda chaperonin | protein | 95 | 3% helix, 40% strand | Q7BGE6 |
| P, R, T, U, V, W, X, 1, 2 | 10 kda chaperonin | protein | 97 | 3% helix, 41% strand | Q7BGE6 |
| Q, S | 10 kda chaperonin | protein | 96 | 3% helix, 43% strand | Q7BGE6 |
| Y | 10 kda chaperonin | protein | 96 | 3% helix, 33% strand | Q7BGE6 |
| Z | 10 kda chaperonin | protein | 95 | 3% helix, 35% strand | Q7BGE6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
- BEF · Beryllium trifluoride ion · ligand · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
- MG · Magnesium ion · metal · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
- K · Potassium ion · metal · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
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 | 289 | 0.85 | 0.96 | 42 | empty |
| 2 | 208 | 0.83 | 0.96 | 39 | empty |
| 3 | 367 | 0.82 | 0.91 | 54 | ADP, BEF, MG, K |
| 4 | 358 | 0.81 | 0.90 | 54 | ADP, BEF, MG, K |
| 5 | 408 | 0.81 | 0.89 | 62 | ADP, BEF, MG, K |
Interfaces
77 interfaces between chains.
- M–N · 1787 Ų buried · 14 hydrogen bonds · protein-protein
- L–M · 1781 Ų buried · 26 hydrogen bonds · protein-protein
- A–G · 1752 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1728 Ų buried · 17 hydrogen bonds · protein-protein
- J–K · 1718 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4PKO · Crystal structure of the Football-shaped GroEL-GroES2-(ADPBeFx)14 complex · the same entry in another collection · chain B against B, 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 Q548M1
- Every structure of UniProt Q7BGE6
- Elsewhere: RCSB PDB 4PKO · PDBe 4PKO · UniProt Q548M1 · UniProt Q7BGE6
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