MolNFT v1 · #58365 · protein
Crystal structure of betac-S lyase from streptococcus anginosus in complex with L-serine: external aldimine form
3B1D: “Crystal structure of betac-S lyase from streptococcus anginosus in complex with L-serine: external aldimine…”. X-ray diffraction, 3 ligands (PLS, PLP, NA), 13 pockets (best druggability 0.81). MolNFT v1 #58365 on GenesisL1: 3D…
- PDB
- 3B1D
- Type
- protein
- Length
- 1,546 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
- PLS, PLP, NA
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Betac-S lyase (EC 4.4.1.8) | protein | 387 | 45% helix, 18% strand | A6BMJ3 |
| C, D | Betac-S lyase (EC 4.4.1.8) | protein | 386 | 45% helix, 18% strand | A6BMJ3 |
Ligands and binding sites
- PLS · [3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-serine · ligand · 4 copies · chains A, B, C, D
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 11 copies · chains A, B, C, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.81 | 0.82 | 133 | EPE, PLS |
| 2 | 499 | 0.75 | 0.83 | 63 | PLP, PLS, EPE |
| 3 | 460 | 0.72 | 0.81 | 63 | EPE, PLS |
| 4 | 267 | 0.67 | 0.83 | 35 | PLP, PLS, EPE |
| 5 | 327 | 0.60 | 0.78 | 42 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2854 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2850 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 530 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 404 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 388 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 covalent (pyridoxal phosphate Schiff base, covalent ligand).
Compared structures
- 3B1D · Crystal structure of betaC-S lyase from Streptococcus anginosus in complex with L-serine… · the same entry in another collection · chain B against B, 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 3B1D · PDBe 3B1D · UniProt A6BMJ3
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