MolNFT v1 · #114138 · protein
Crystal structure of L-tryptophan dehydrogenase from nostoc punctiforme
5B37: “Crystal structure of L-tryptophan dehydrogenase from nostoc punctiforme”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #114138 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5B37
- Type
- protein
- Length
- 1,996 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan dehydrogenase
- EC
- 1.4.1.19
- UniProt
- W8CV45
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan dehydrogenase (EC 1.4.1.19) | protein | 330 | 47% helix, 17% strand | W8CV45 |
| B | Tryptophan dehydrogenase (EC 1.4.1.19) | protein | 336 | 48% helix, 15% strand | W8CV45 |
| C | Tryptophan dehydrogenase (EC 1.4.1.19) | protein | 333 | 48% helix, 16% strand | W8CV45 |
| D | Tryptophan dehydrogenase (EC 1.4.1.19) | protein | 328 | 50% helix, 16% strand | W8CV45 |
| E | Tryptophan dehydrogenase (EC 1.4.1.19) | protein | 335 | 47% helix, 16% strand | W8CV45 |
| F | Tryptophan dehydrogenase (EC 1.4.1.19) | protein | 334 | 48% helix, 14% strand | W8CV45 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.79 | 0.81 | 75 | empty |
| 2 | 1092 | 0.79 | 0.80 | 77 | empty |
| 3 | 1079 | 0.78 | 0.80 | 81 | empty |
| 4 | 279 | 0.75 | 0.87 | 36 | empty |
| 5 | 331 | 0.74 | 0.86 | 41 | empty |
Interfaces
6 interfaces between chains.
- D–F · 1092 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 1040 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 1026 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 296 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 239 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5B37 · Crystal structure of L-tryptophan dehydrogenase from Nostoc punctiforme · 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 W8CV45
- Elsewhere: RCSB PDB 5B37 · PDBe 5B37 · UniProt W8CV45
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