MolNFT v1 · #146384 · protein
Trypanosoma brucei deoxyhypusine synthase
6DFT: “Trypanosoma brucei deoxyhypusine synthase”. X-ray diffraction, 2 ligands (NAD, NA), 20 pockets (best druggability 0.91). MolNFT v1 #146384 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DFT
- Type
- protein
- Length
- 4,144 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyhypusine synthase; Deoxyhypusine synthase regulatory subunit
- EC
- 2.5.1.46
- UniProt
- Q38BX0, Q4GZD1
- Ligands
- NAD, NA
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 12 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyhypusine synthase (EC 2.5.1.46) | protein | 384 | 47% helix, 14% strand | Q38BX0 |
| B | Deoxyhypusine synthase regulatory subunit (EC 2.5.1.46) | protein | 318 | 52% helix, 13% strand | Q4GZD1 |
| C | Deoxyhypusine synthase (EC 2.5.1.46) | protein | 369 | 48% helix, 15% strand | Q38BX0 |
| D | Deoxyhypusine synthase regulatory subunit (EC 2.5.1.46) | protein | 320 | 51% helix, 13% strand | Q4GZD1 |
| E | Deoxyhypusine synthase (EC 2.5.1.46) | protein | 370 | 50% helix, 14% strand | Q38BX0 |
| F | Deoxyhypusine synthase regulatory subunit (EC 2.5.1.46) | protein | 321 | 51% helix, 13% strand | Q4GZD1 |
| G | Deoxyhypusine synthase (EC 2.5.1.46) | protein | 367 | 48% helix, 12% strand | Q38BX0 |
| H | Deoxyhypusine synthase regulatory subunit (EC 2.5.1.46) | protein | 317 | 51% helix, 13% strand | Q4GZD1 |
| I | Deoxyhypusine synthase (EC 2.5.1.46) | protein | 364 | 49% helix, 13% strand | Q38BX0 |
| J | Deoxyhypusine synthase regulatory subunit (EC 2.5.1.46) | protein | 316 | 52% helix, 13% strand | Q4GZD1 |
| K | Deoxyhypusine synthase (EC 2.5.1.46) | protein | 381 | 47% helix, 14% strand | Q38BX0 |
| L | Deoxyhypusine synthase regulatory subunit (EC 2.5.1.46) | protein | 317 | 50% helix, 13% strand | Q4GZD1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 12 copies · chains A, B, D, C, E, F, G, H, I, J, L, K
- NA · Sodium ion · metal · chains A, B
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 | 1191 | 0.91 | 0.93 | 176 | NAD |
| 2 | 625 | 0.88 | 0.93 | 99 | NAD |
| 3 | 957 | 0.87 | 0.89 | 117 | NA, NAD |
| 4 | 535 | 0.87 | 0.93 | 99 | NAD |
| 5 | 775 | 0.87 | 0.90 | 101 | NAD |
Interfaces
27 interfaces between chains.
- K–L · 2895 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 2831 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 2828 Ų buried · 37 hydrogen bonds · protein-protein
- J–K · 2741 Ų buried · 45 hydrogen bonds · protein-protein
- I–L · 2709 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6DFT · Trypanosoma brucei deoxyhypusine synthase · the same entry in another collection · chain L against L, 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 Q38BX0
- Every structure of UniProt Q4GZD1
- Elsewhere: RCSB PDB 6DFT · PDBe 6DFT · UniProt Q38BX0 · UniProt Q4GZD1
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