MolNFT v1 · #4320 · protein
Crystal structure of a groel (apical domain) and a dodecameric peptide complex
1DKD: “Crystal structure of a groel (apical domain) and a dodecameric peptide complex”. X-ray diffraction, 1 pocket (best druggability 0.56). MolNFT v1 #4320 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1DKD
- Type
- protein
- Length
- 629 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Groel; 12-mer peptide
- UniProt
- P0A6F5
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Groel | protein | 146 | 34% helix, 29% strand | P0A6F5 |
| E, F, H | 12-mer peptide | protein | 11 | 0% helix, 36% strand | — |
| G | 12-mer peptide | protein | 12 | 0% helix, 33% strand | — |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.56 | 0.78 | 39 | empty |
Interfaces
9 interfaces between chains.
- A–C · 538 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 504 Ų buried · 5 hydrogen bonds · protein-protein
- D–H · 493 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 489 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 477 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1DKD · Crystal structure of a groel (apical domain) and a dodecameric peptide complex · the same entry in another collection · chain H against H, TM-score 1.00
- P0A6F5 · AlphaFold monomer V2.0 prediction for 60 kda chaperonin (P0A6F5) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P0A6F5
- Elsewhere: RCSB PDB 1DKD · PDBe 1DKD · UniProt P0A6F5
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