SMTL ID : 8qop.1

Capra hircus reactive intermediate deaminase A - K78A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-hexamer

Ligands

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 8 residues within 4Å: Chain A: G.22, Y.24, P.119 Chain E: F.92, N.96, R.110, A.111, A.112 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:R.110, E:R.110, E:R.110 Water bridges: E:A.112, E:A.112 EDO.4: 8 residues within 4Å: Chain A: F.92, N.96, R.110, A.111, A.112 Chain C: G.22, Y.24, P.119 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.110, A:R.110, A:R.110 Water bridges: A:A.112, A:A.112 EDO.7: 8 residues within 4Å: Chain C: F.92, N.96, R.110, A.111, A.112 Chain E: G.22, Y.24, P.119 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.110, C:R.110, C:R.110 Water bridges: C:A.112, C:A.112

6 x NA: SODIUM ION(Non-functional Binders)

NA.2: 1 residues within 4Å: Chain B: R.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.123, B:R.123 NA.3: 2 residues within 4Å: Chain B: R.110 Chain F: Y.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.110, B:R.110, B:R.110 NA.5: 1 residues within 4Å: Chain D: R.123 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.123, D:R.123 NA.6: 2 residues within 4Å: Chain B: Y.24 Chain D: R.110 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.110, D:R.110, D:R.110 NA.8: 1 residues within 4Å: Chain F: R.123 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.123, F:R.123 NA.9: 2 residues within 4Å: Chain D: Y.24 Chain F: R.110 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.110, F:R.110, F:R.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rizzi, G. et al., Site-directed mutagenesis reveals the interplay between stability, structure, and enzymatic activity in RidA from Capra hircus. Protein Sci. (2024)

Release Date

2024-06-26

Peptides

2-iminobutanoate/2-iminopropanoate deaminase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

2-iminobutanoate/2-iminopropanoate deaminase