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MolNFT v1 · #49001 · protein

Crystal structure of the second tetrahedral intermediates of sgpb at pH 4.2

2QA9 · Streptogrisin-B: “Crystal structure of the second tetrahedral intermediates of sgpb at pH 4.2”. X-ray diffraction, 2 ligands (CL, SO4). MolNFT v1 #49001 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
2QA9
Type
protein
Length
189 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Streptogrisin-B; 4-mer peptide daiy
EC
3.4.21.81
UniProt
P00777
Ligands
CL, SO4

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
EStreptogrisin-B (EC 3.4.21.81)protein1856% helix, 52% strandP00777
I4-mer peptide daiyprotein40% helix, 50% strand—

Ligands and binding sites

  • CL · Chloride ion · ion · 2 copies · chains E
  • SO4 · Sulfate ion · ion · 2 copies · chains E
  • EDO · 1,2-ethanediol · additive · 4 copies · chains E, I
  • GOL · Glycerol · additive · chains E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

1 interface between chains.

  • E–I · 411 Ų buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

  • 2QA9 · Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2 · the same entry in another collection · chain E against E, TM-score 1.00
  • P00777 · AlphaFold monomer V2.0 prediction for streptogrisin-B (P00777) · a predicted model of the same protein · chain E against A, TM-score 0.99

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