MolNFT v1 · #58364 · protein
Crystal structure of betac-S lyase from streptococcus anginosus: internal aldimine form
3B1C: “Crystal structure of betac-S lyase from streptococcus anginosus: internal aldimine form”. X-ray diffraction, 2 ligands (PLP, SO4), 13 pockets (best druggability 0.81). MolNFT v1 #58364 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3B1C
- Type
- protein
- Length
- 1,545 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Betac-S lyase
- EC
- 4.4.1.8
- UniProt
- A6BMJ3
- Ligands
- PLP, SO4
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Betac-S lyase (EC 4.4.1.8) | protein | 387 | 45% helix, 18% strand | A6BMJ3 |
| B | Betac-S lyase (EC 4.4.1.8) | protein | 386 | 46% helix, 18% strand | A6BMJ3 |
| D | Betac-S lyase (EC 4.4.1.8) | protein | 385 | 45% helix, 18% strand | A6BMJ3 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 14 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.81 | 0.82 | 103 | GOL, PLP, SO4 |
| 2 | 519 | 0.75 | 0.83 | 62 | GOL, PLP, SO4 |
| 3 | 437 | 0.68 | 0.80 | 55 | PLP, SO4 |
| 4 | 390 | 0.67 | 0.80 | 52 | PLP, SO4 |
| 5 | 307 | 0.59 | 0.78 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2872 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2866 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 470 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 412 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 404 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3B1C · Crystal structure of betaC-S lyase from Streptococcus anginosus: Internal aldimine form · 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 A6BMJ3
- Elsewhere: RCSB PDB 3B1C · PDBe 3B1C · UniProt A6BMJ3
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