Research workbench
Crystal structure of C terminal truncated hadbc (3R-hydroxyacyl-acp dehydratase) complex from mycobacterium tuberculosis
Analyse Crystal structure of C terminal truncated hadbc (3R-hydroxyacyl-acp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZY8
- Type
- protein
- Length
- 553 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0336 protein RV0637; 3-hydroxyacyl-acp dehydratase
- UniProt
- P9WFJ9, L0T618
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0336 protein RV0637 | protein | 133 | 25% helix, 36% strand | P9WFJ9 |
| B | 3-hydroxyacyl-acp dehydratase | protein | 141 | 30% helix, 35% strand | L0T618 |
| C | UPF0336 protein RV0637 | protein | 137 | 24% helix, 38% strand | P9WFJ9 |
| D | 3-hydroxyacyl-acp dehydratase | protein | 142 | 30% helix, 35% strand | L0T618 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.78 | 0.80 | 132 | empty |
| 2 | 79 | 0.48 | 0.82 | 15 | empty |
| 3 | 55 | 0.38 | 0.80 | 14 | empty |
| 4 | 78 | 0.35 | 0.75 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1377 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1330 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 606 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 539 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ZY8 · Crystal structure of C terminal truncated HadBC (3R-Hydroxyacyl-ACP Dehydratase) complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WFJ9 · AlphaFold monomer V2.0 prediction for UPF0336 protein RV0637 (P9WFJ9) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P9WFJ9
- Every structure of UniProt L0T618
- Elsewhere: RCSB PDB 5ZY8 · PDBe 5ZY8 · UniProt P9WFJ9 · UniProt L0T618
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