SMTL ID : 8qov.1

Capra hircus reactive intermediate deaminase A mutant - I126Y

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

Ligands

3 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 5 residues within 4Å: Chain A: G.1, S.2, H.3, M.4 Chain C: P.134 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.3 NI.4: 5 residues within 4Å: Chain C: G.1, S.2, H.3, M.4 Chain E: P.134 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.3 NI.7: 5 residues within 4Å: Chain A: P.134 Chain E: G.1, S.2, H.3, M.4 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.3

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

EDO.2: 6 residues within 4Å: Chain B: G.73, T.77, N.78, G.133, P.134, L.135 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.78, B:G.133, B:L.135 EDO.5: 6 residues within 4Å: Chain D: G.73, T.77, N.78, G.133, P.134, L.135 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.78, D:G.133, D:L.135 EDO.8: 6 residues within 4Å: Chain F: G.73, T.77, N.78, G.133, P.134, L.135 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.78, F:G.133, F:L.135

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 11 residues within 4Å: Chain B: I.21, Y.24, S.37, G.38, L.40, P.119, E.125 Chain F: F.92, R.110, A.111, A.112 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:R.110, F:R.110, B:G.38 Water bridges: F:A.112, F:A.112 PEG.6: 11 residues within 4Å: Chain B: F.92, R.110, A.111, A.112 Chain D: I.21, Y.24, S.37, G.38, L.40, P.119, E.125 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.110, B:R.110, D:G.38 Water bridges: B:A.112, B:A.112 PEG.9: 11 residues within 4Å: Chain D: F.92, R.110, A.111, A.112 Chain F: I.21, Y.24, S.37, G.38, L.40, P.119, E.125 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:R.110, D:R.110, F:G.38 Water bridges: D:A.112, D:A.112

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