Research workbench
Crystal structure of mycobacterium tuberculosis alkylperoxidase ahpd
Analyse Crystal structure of mycobacterium tuberculosis alkylperoxidase ahpd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GU9
- Type
- protein
- Length
- 2,052 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkylhydroperoxidase D
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, J | Alkylhydroperoxidase D | protein | 172 | 75% helix, 0% strand | — |
| B, E, I, K | Alkylhydroperoxidase D | protein | 173 | 75% helix, 0% strand | — |
| C, G | Alkylhydroperoxidase D | protein | 168 | 76% helix, 0% strand | — |
| F | Alkylhydroperoxidase D | protein | 169 | 76% helix, 0% strand | — |
| H | Alkylhydroperoxidase D | protein | 171 | 74% helix, 0% strand | — |
| L | Alkylhydroperoxidase D | protein | 168 | 72% helix, 0% strand | — |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.81 | 0.84 | 80 | empty |
| 2 | 760 | 0.81 | 0.85 | 77 | empty |
| 3 | 793 | 0.81 | 0.84 | 77 | empty |
| 4 | 774 | 0.81 | 0.84 | 77 | empty |
| 5 | 571 | 0.64 | 0.75 | 51 | empty |
Interfaces
20 interfaces between chains.
- J–K · 1593 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 1567 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1559 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1551 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1512 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 1GU9 · Crystal Structure of Mycobacterium tuberculosis Alkylperoxidase AhpD · the same entry in another collection · chain I against I, 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
- Elsewhere: RCSB PDB 1GU9 · PDBe 1GU9
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