MolNFT v1 · #84614 · protein
Visualizing groel-es in the act of encapsulating a non-native substrate protein
3ZQ1 · 60 kda chaperonin: “Visualizing groel-es in the act of encapsulating a non-native substrate protein”. Electron microscopy, 2 ligands (ADP, MG), 20 pockets (best druggability 0.83). MolNFT v1 #84614 on GenesisL1: 3D structure…
- PDB
- 3ZQ1
- Type
- protein
- Length
- 8,015 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 60 kda chaperonin; 10 kda chaperonin
- UniProt
- P0A6F5, P0A6F9
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 44% helix, 20% 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, 16% strand | P0A6F5 |
| O, P, Q, R, S, T, U | 10 kda chaperonin | protein | 97 | 3% helix, 39% strand | P0A6F9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 7 copies · chains A, B, C, D, E, F, G
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, F, G
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 | 419 | 0.83 | 0.91 | 62 | MG, ADP |
| 2 | 383 | 0.82 | 0.91 | 57 | MG, ADP |
| 3 | 398 | 0.82 | 0.90 | 57 | MG, ADP |
| 4 | 430 | 0.82 | 0.90 | 62 | MG, ADP |
| 5 | 377 | 0.81 | 0.90 | 60 | MG, ADP |
Interfaces
49 interfaces between chains.
- E–F · 1536 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 1513 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1511 Ų buried · 5 hydrogen bonds · protein-protein
- A–G · 1476 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1452 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3ZQ1 · Visualizing GroEL-ES in the Act of Encapsulating a Non-Native Substrate Protein · the same entry in another collection · chain K against K, 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 P0A6F5
- Every structure of UniProt P0A6F9
- Elsewhere: RCSB PDB 3ZQ1 · PDBe 3ZQ1 · UniProt P0A6F5 · UniProt P0A6F9
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