Research workbench
Crystal structure of brugia malayi deoxyhypusine synthase (dhps)
Analyse Crystal structure of brugia malayi deoxyhypusine synthase (dhps) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W3Z
- Type
- protein
- Length
- 1,381 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bma-dhps-1, isoform a
- UniProt
- A0A0J9XTC4
- Ligands
- NAD, CL
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bma-dhps-1, isoform a | protein | 350 | 51% helix, 13% strand | A0A0J9XTC4 |
| B | Bma-dhps-1, isoform a | protein | 333 | 51% helix, 14% strand | A0A0J9XTC4 |
| C | Bma-dhps-1, isoform a | protein | 352 | 50% helix, 13% strand | A0A0J9XTC4 |
| D | Bma-dhps-1, isoform a | protein | 346 | 50% helix, 13% strand | A0A0J9XTC4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, D, B, C
- CL · Chloride ion · ion · chains B, C
- GOL · Glycerol · additive · 5 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.85 | 0.95 | 79 | NAD |
| 2 | 237 | 0.83 | 0.95 | 52 | empty |
| 3 | 217 | 0.83 | 0.96 | 51 | NAD |
| 4 | 172 | 0.80 | 0.96 | 43 | NAD |
| 5 | 115 | 0.77 | 0.95 | 41 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3700 Ų buried · 54 hydrogen bonds · protein-protein
- B–D · 3017 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 2917 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 2613 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 735 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6W3Z · Crystal Structure of Brugia malayi Deoxyhypusine synthase (DHPS) · 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 A0A0J9XTC4
- Elsewhere: RCSB PDB 6W3Z · PDBe 6W3Z · UniProt A0A0J9XTC4
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