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Crystal structure of apo groel
Analyse Crystal structure of apo groel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XCK
- Type
- protein
- Length
- 7,336 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 60 kda chaperonin
- UniProt
- P06139
- Ligands
- K, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 19% 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 | 51% helix, 19% strand | P06139 |
Ligands and binding sites
- K · Potassium ion · metal · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
- SO4 · Sulfate ion · ion · 43 copies · chains A, L, B, C, K, D, J, E, F, G, H, I, M, N
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 31 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
- PEG · Di(hydroxyethyl)ether · additive · chains E, I
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 | 1168 | 0.78 | 0.80 | 119 | K |
| 2 | 1190 | 0.78 | 0.80 | 96 | empty |
| 3 | 1091 | 0.78 | 0.80 | 108 | empty |
| 4 | 511 | 0.76 | 0.84 | 56 | empty |
| 5 | 684 | 0.76 | 0.82 | 56 | empty |
Interfaces
28 interfaces between chains.
- H–N · 1827 Ų buried · 19 hydrogen bonds · protein-protein
- H–I · 1768 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1751 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 1731 Ų buried · 18 hydrogen bonds · protein-protein
- M–N · 1731 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1XCK · Crystal structure of apo GroEL · 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 P06139
- Elsewhere: RCSB PDB 1XCK · PDBe 1XCK · UniProt P06139
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