Research workbench
Beta-hydroxyacyl-acyl carrier protein dehydratase (fabz) from plasmodium falciparum in complex with NAS21
Analyse Beta-hydroxyacyl-acyl carrier protein dehydratase (fabz) from plasmodium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AZ8
- Type
- protein
- Length
- 3,453 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hydroxyacyl-acp dehydratase
- EC
- 4.2.1.-
- UniProt
- Q965D7
- Ligands
- S21, CL, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 11 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, N, X | Beta-hydroxyacyl-acp dehydratase (EC 4.2.1.-) | protein | 145 | 18% helix, 41% strand | Q965D7 |
| B, H | Beta-hydroxyacyl-acp dehydratase (EC 4.2.1.-) | protein | 141 | 21% helix, 43% strand | Q965D7 |
| C, O, U | Beta-hydroxyacyl-acp dehydratase (EC 4.2.1.-) | protein | 144 | 24% helix, 39% strand | Q965D7 |
| D | Beta-hydroxyacyl-acp dehydratase (EC 4.2.1.-) | protein | 140 | 19% helix, 39% strand | Q965D7 |
| E | Beta-hydroxyacyl-acp dehydratase (EC 4.2.1.-) | protein | 143 | 18% helix, 39% strand | Q965D7 |
| F, L, R, S | Beta-hydroxyacyl-acp dehydratase (EC 4.2.1.-) | protein | 146 | 18% helix, 41% strand | Q965D7 |
| I | Beta-hydroxyacyl-acp dehydratase (EC 4.2.1.-) | protein | 143 | 22% helix, 40% strand | Q965D7 |
| J, V | Beta-hydroxyacyl-acp dehydratase (EC 4.2.1.-) | protein | 144 | 22% helix, 38% strand | Q965D7 |
| K, M, P | Beta-hydroxyacyl-acp dehydratase (EC 4.2.1.-) | protein | 145 | 19% helix, 39% strand | Q965D7 |
| Q, W | Beta-hydroxyacyl-acp dehydratase (EC 4.2.1.-) | protein | 142 | 18% helix, 40% strand | Q965D7 |
| T | Beta-hydroxyacyl-acp dehydratase (EC 4.2.1.-) | protein | 142 | 21% helix, 39% strand | Q965D7 |
Ligands and binding sites
- S21 · 4,4,4-trifluoro-1-(4-nitrophenyl)butane-1,3-dione · ligand · 4 copies · chains C, D, E, F, O, P, Q, R
- CL · Chloride ion · ion · 17 copies · chains A, B, C, D, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
- PO4 · Phosphate ion · ion · chains E, F
- PEG · Di(hydroxyethyl)ether · additive · 29 copies · chains A, B, C, F, E, G, H, I, J, K, L, N, O, R, P, Q, S, T, V, U, W, X
- GOL · Glycerol · additive · 13 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, R, Q, S, T, V, U, W, X
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 | 882 | 0.83 | 0.84 | 93 | GOL, PEG |
| 2 | 959 | 0.81 | 0.82 | 90 | GOL |
| 3 | 1009 | 0.81 | 0.82 | 95 | GOL, PEG |
| 4 | 1067 | 0.80 | 0.81 | 93 | GOL, PEG |
| 5 | 1033 | 0.77 | 0.79 | 123 | CL |
Interfaces
36 interfaces between chains.
- M–N · 1445 Ų buried · 15 hydrogen bonds · protein-protein
- Q–R · 1445 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1432 Ų buried · 14 hydrogen bonds · protein-protein
- W–X · 1418 Ų buried · 16 hydrogen bonds · protein-protein
- O–P · 1415 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3AZ8 · Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Plasmodium falciparum in… · 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 Q965D7
- Elsewhere: RCSB PDB 3AZ8 · PDBe 3AZ8 · UniProt Q965D7
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