MolNFT v1 · #114082 · protein
Crystal structure of K42A mutant of cystathionine beta-synthase from lactobacillus plantarum in a complex with L-methionine
5B1I: “Crystal structure of K42A mutant of cystathionine beta-synthase from lactobacillus plantarum in a complex…”. X-ray diffraction, 2 ligands (AA5, SO4), 20 pockets (best druggability 0.86). MolNFT v1 #114082 on GenesisL1: 3D structure…
- PDB
- 5B1I
- Type
- protein
- Length
- 2,424 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-synthase
- EC
- 4.2.1.22
- UniProt
- F9UT54
- Ligands
- AA5, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 303 | 42% helix, 19% strand | F9UT54 |
Ligands and binding sites
- AA5 · N-[(3-hydroxy-2-methyl-5-{[(trihydroxyphosphoranyl)oxy]methyl}pyridin-4-yl)methylene]methionine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D, E, F, G, H
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 | 808 | 0.86 | 0.88 | 61 | empty |
| 2 | 654 | 0.83 | 0.87 | 47 | empty |
| 3 | 158 | 0.80 | 0.96 | 34 | empty |
| 4 | 1008 | 0.80 | 0.81 | 71 | empty |
| 5 | 151 | 0.80 | 0.96 | 34 | empty |
Interfaces
13 interfaces between chains.
- E–F · 1741 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1726 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1722 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 1698 Ų buried · 27 hydrogen bonds · protein-protein
- D–H · 781 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5B1I · Crystal structure of K42A mutant of cystathionine beta-synthase from Lactobacillus… · 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 F9UT54
- Elsewhere: RCSB PDB 5B1I · PDBe 5B1I · UniProt F9UT54
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