MolNFT v2 · #222749 · protein
Proteus vulgaris tryptophan indole-lyase complexed with L-ethionine
8V4A · Tryptophanase: “Proteus vulgaris tryptophan indole-lyase complexed with L-ethionine”. X-ray diffraction at 1.96, 3 ligands (YAE, YAR, K), 20 pockets (best druggability 0.80). MolNFT v2 #222749 on GenesisL1: 3D structure, binding…
- PDB
- 8V4A
- Type
- protein
- Length
- 1,863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.96
- Source
- Proteus vulgaris
- Molecule
- Tryptophanase
- EC
- 4.1.99.1
- UniProt
- P28796
- Ligands
- YAE, YAR, K
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.96 · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Tryptophanase (EC 4.1.99.1) | protein | 466 | 45% helix, 16% strand | P28796 |
| C | Tryptophanase (EC 4.1.99.1) | protein | 465 | 45% helix, 16% strand | P28796 |
Ligands and binding sites
- YAE · (E)-S-ethyl-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-homocysteine · ligand · 2 copies · chains A, B, C, D
- YAR · (2E)-4-(ethylsulfanyl)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}butanoic acid · ligand · 2 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 128 | 0.80 | 0.98 | 34 | YAR |
| 2 | 130 | 0.80 | 0.98 | 35 | YAR |
| 3 | 133 | 0.79 | 0.97 | 35 | YAE |
| 4 | 938 | 0.79 | 0.81 | 92 | YAE |
| 5 | 222 | 0.71 | 0.87 | 47 | DMS |
Interfaces
6 interfaces between chains.
- A–B · 2340 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2322 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1771 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 1751 Ų buried · 41 hydrogen bonds · protein-protein
- A–D · 395 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- P28796 · AlphaFold monomer V2.0 prediction for tryptophanase (P28796) · a predicted model of the same protein · chain C 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 P28796
- Elsewhere: RCSB PDB 8V4A · PDBe 8V4A · UniProt P28796
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.