MolNFT v1 · #179387 · protein
P. falciparum CPN60 D474A mutant bound to ATP
7K3Z · 60 kda chaperonin: “P. falciparum CPN60 D474A mutant bound to ATP”. X-ray diffraction, 2 ligands (ATP, MG), 20 pockets (best druggability 0.83). MolNFT v1 #179387 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7K3Z
- Type
- protein
- Length
- 3,934 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 60 kda chaperonin
- UniProt
- Q8I0V3
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 60 kda chaperonin | protein | 564 | 49% helix, 16% strand | Q8I0V3 |
| B | 60 kda chaperonin | protein | 560 | 48% helix, 16% strand | Q8I0V3 |
| C | 60 kda chaperonin | protein | 562 | 49% helix, 14% strand | Q8I0V3 |
| D | 60 kda chaperonin | protein | 562 | 49% helix, 15% strand | Q8I0V3 |
| E | 60 kda chaperonin | protein | 562 | 48% helix, 15% strand | Q8I0V3 |
| F | 60 kda chaperonin | protein | 561 | 49% helix, 15% strand | Q8I0V3 |
| G | 60 kda chaperonin | protein | 563 | 48% helix, 14% strand | Q8I0V3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · 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 | 951 | 0.83 | 0.84 | 110 | MG, ATP |
| 2 | 847 | 0.81 | 0.83 | 93 | MG, ATP |
| 3 | 989 | 0.81 | 0.82 | 108 | MG, ATP |
| 4 | 1026 | 0.81 | 0.82 | 118 | MG, ATP |
| 5 | 567 | 0.79 | 0.85 | 68 | MG, ATP |
Interfaces
8 interfaces between chains.
- B–C · 2042 Ų buried · 25 hydrogen bonds · protein-protein
- A–G · 2010 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1976 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 1931 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1920 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 7K3Z · P. falciparum Cpn60 D474A mutant bound to ATP · 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 Q8I0V3
- Elsewhere: RCSB PDB 7K3Z · PDBe 7K3Z · UniProt Q8I0V3
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