Research workbench
Crystal structure of the mycobacterium tuberculosis chaperonin 10 tetradecamer
Analyse Crystal structure of the mycobacterium tuberculosis chaperonin 10 tetradecamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P3H
- Type
- protein
- Length
- 1,379 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 10 kda chaperonin
- UniProt
- P09621
- Ligands
- CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F, G, H, M, N | 10 kda chaperonin | protein | 99 | 3% helix, 48% strand | P09621 |
| B, C, E, I, J, K, L | 10 kda chaperonin | protein | 98 | 3% helix, 47% strand | P09621 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.86 | 0.88 | 148 | empty |
| 2 | 845 | 0.83 | 0.86 | 79 | empty |
| 3 | 1054 | 0.82 | 0.83 | 111 | empty |
| 4 | 717 | 0.70 | 0.78 | 88 | empty |
| 5 | 291 | 0.65 | 0.81 | 36 | empty |
Interfaces
32 interfaces between chains.
- D–N · 850 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 818 Ų buried · 11 hydrogen bonds · protein-protein
- K–L · 817 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 815 Ų buried · 15 hydrogen bonds · protein-protein
- H–I · 812 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1P3H · Crystal Structure of the Mycobacterium tuberculosis chaperonin 10 tetradecamer · 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 P09621
- Elsewhere: RCSB PDB 1P3H · PDBe 1P3H · UniProt P09621
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