Research workbench
Crystal structure of the chaperonin GP146 from the bacteriophage el 2 (pseudomonas aeruginosa) in presence of ATP-befx, crystal form II
Analyse Crystal structure of the chaperonin GP146 from the bacteriophage el 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TMU
- Type
- protein
- Length
- 3,828 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative groel-like chaperonine protein
- UniProt
- Q2Z0T5
- Ligands
- ATP, ADP, MG, K
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative groel-like chaperonine protein | protein | 550 | 52% helix, 15% strand | Q2Z0T5 |
| B, D, G | Putative groel-like chaperonine protein | protein | 545 | 52% helix, 15% strand | Q2Z0T5 |
| E | Putative groel-like chaperonine protein | protein | 549 | 52% helix, 15% strand | Q2Z0T5 |
| F | Putative groel-like chaperonine protein | protein | 544 | 52% helix, 15% strand | Q2Z0T5 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, C, E, G
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains B, D, F
- MG · Magnesium ion · metal · 4 copies · chains A, C, E, G
- K · Potassium ion · metal · 4 copies · chains A, C, E, 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 | 495 | 0.81 | 0.87 | 51 | MG, K, ATP |
| 2 | 504 | 0.80 | 0.87 | 51 | MG, K, ATP |
| 3 | 526 | 0.79 | 0.86 | 57 | MG, K, ATP |
| 4 | 1080 | 0.79 | 0.80 | 97 | MG, K, ATP |
| 5 | 675 | 0.74 | 0.80 | 55 | ADP |
Interfaces
7 interfaces between chains.
- A–B · 1509 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1393 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1373 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1353 Ų buried · 15 hydrogen bonds · protein-protein
- A–G · 1347 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6TMU · Crystal structure of the chaperonin gp146 from the bacteriophage EL 2 (Pseudomonas… · 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 Q2Z0T5
- Elsewhere: RCSB PDB 6TMU · PDBe 6TMU · UniProt Q2Z0T5
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