MolNFT v1 · #18132 · protein
Groel-groes-ADP
1PF9 · Groel protein: “Groel-groes-ADP”. X-ray diffraction, 2 ligands (ADP, MG), 20 pockets (best druggability 0.80). MolNFT v1 #18132 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1PF9
- Type
- protein
- Length
- 8,015 residues
- Chains
- 21
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Groel protein; Groes protein
- UniProt
- P06139, P05380
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 43% 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 | Groel protein | protein | 524 | 50% helix, 17% strand | P06139 |
| O, P, Q, R, S, T, U | Groes protein | protein | 97 | 3% helix, 36% strand | P05380 |
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 | 343 | 0.80 | 0.90 | 52 | MG, ADP |
| 2 | 365 | 0.80 | 0.89 | 56 | MG, ADP |
| 3 | 331 | 0.80 | 0.90 | 51 | MG, ADP |
| 4 | 391 | 0.79 | 0.88 | 57 | MG, ADP |
| 5 | 359 | 0.78 | 0.88 | 55 | MG, ADP |
Interfaces
47 interfaces between chains.
- M–N · 1733 Ų buried · 26 hydrogen bonds · protein-protein
- L–M · 1723 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 1719 Ų buried · 24 hydrogen bonds · protein-protein
- K–L · 1704 Ų buried · 24 hydrogen bonds · protein-protein
- I–J · 1702 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1PF9 · GroEL-GroES-ADP · 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
- Every structure of UniProt P05380
- Elsewhere: RCSB PDB 1PF9 · PDBe 1PF9 · UniProt P06139 · UniProt P05380
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