Research workbench
Crystal structure of the football-shaped groel-GROES2-(ADPBEFX)14 complex containing substrate rubisco
Analyse Crystal structure of the football-shaped groel-GROES2-(ADPBEFX)14 complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PKN
- Type
- protein
- Length
- 8,689 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 0.83
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, A, B, F, E, C, D, K, J, I, L, M, H, N | 60 kda chaperonin | protein | 524 | 49% helix, 17% strand | Q548M1 |
| O, P, Q, U, T, R, S, Z, 2, 1 | 10 kda chaperonin | protein | 97 | 3% helix, 45% strand | Q7BGE6 |
| X | 10 kda chaperonin | protein | 95 | 3% helix, 40% strand | Q7BGE6 |
| W | 10 kda chaperonin | protein | 96 | 3% helix, 43% strand | Q7BGE6 |
| V, Y | 10 kda chaperonin | protein | 96 | 3% helix, 36% strand | Q7BGE6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 14 copies · chains G, A, B, F, E, C, D, K, J, I, L, M, H, N
- BEF · Beryllium trifluoride ion · ligand · 14 copies · chains G, A, B, F, E, C, D, K, J, I, L, M, H, N
- MG · Magnesium ion · metal · 14 copies · chains G, A, B, F, E, C, D, K, J, I, L, M, H, N
- K · Potassium ion · metal · 14 copies · chains G, A, B, F, E, C, D, K, J, I, L, M, H, 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 | 177 | 0.83 | 0.97 | 29 | empty |
| 2 | 396 | 0.81 | 0.90 | 56 | ADP, BEF, MG, K |
| 3 | 150 | 0.81 | 0.97 | 35 | empty |
| 4 | 362 | 0.81 | 0.90 | 54 | ADP, BEF, MG, K |
| 5 | 376 | 0.81 | 0.90 | 54 | ADP, BEF, MG, K |
Interfaces
78 interfaces between chains.
- F–E · 1775 Ų buried · 19 hydrogen bonds · protein-protein
- E–D · 1760 Ų buried · 19 hydrogen bonds · protein-protein
- M–N · 1757 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1745 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1743 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4PKN · Crystal structure of the football-shaped GroEL-GroES2-(ADPBeFx)14 complex containing… · the same entry in another collection · chain C against C, 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 4PKN · PDBe 4PKN · UniProt Q548M1 · UniProt Q7BGE6
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