Research workbench
P113S mutant of E. COLI cystathionine beta-lyase metc inhibited by reaction with L-ala-P
Analyse P113S mutant of E. COLI cystathionine beta-lyase metc inhibited by reaction… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ITX
- Type
- protein
- Length
- 783 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-lyase metc
- EC
- 4.4.1.8
- UniProt
- P06721
- Ligands
- IN5, CA
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine beta-lyase metc (EC 4.4.1.8) | protein | 391 | 41% helix, 16% strand | P06721 |
| B | Cystathionine beta-lyase metc (EC 4.4.1.8) | protein | 392 | 41% helix, 16% strand | P06721 |
Ligands and binding sites
- IN5 · {1-[(3-hydroxy-methyl-5-phosphonooxy-methyl-pyridin-4-ylmethyl)-amino]-ethyl}-phosphonic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.68 | 0.88 | 27 | empty |
| 2 | 162 | 0.68 | 0.87 | 26 | empty |
| 3 | 184 | 0.60 | 0.82 | 36 | IN5 |
| 4 | 184 | 0.60 | 0.82 | 34 | IN5 |
| 5 | 50 | 0.44 | 0.84 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 789 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4ITX · P113S mutant of E. coli Cystathionine beta-lyase MetC inhibited by reaction with L-Ala-P · the same entry in another collection · chain A against A, TM-score 1.00
- P06721 · AlphaFold monomer V2.0 prediction for cystathionine beta-lyase metc (P06721) · a predicted model of the same protein · chain B 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 P06721
- Elsewhere: RCSB PDB 4ITX · PDBe 4ITX · UniProt P06721
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.