SMTL ID : 6tcd.2 (1 other biounit)

Crystal structure of Salmo salar RidA-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

homo-trimer

Ligands

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: F.92, R.110, A.111, A.112 Chain B: Y.24, G.38 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.24 Water bridges: B:Y.24, A:A.112, A:A.112 Salt bridges: A:R.110 ACT.2: 7 residues within 4Å: Chain B: R.110, A.111, A.112 Chain C: Y.24, G.38, E.125 Ligands: SO4.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Water bridges: B:R.110 Salt bridges: B:R.110 Hydrophobic interactions: C:Y.24 ACT.3: 6 residues within 4Å: Chain A: Y.24, G.38 Chain C: F.92, R.110, A.111, A.112 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Water bridges: C:A.112, C:A.112 Salt bridges: C:R.110 Hydrophobic interactions: A:Y.24

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 6 residues within 4Å: Chain C: R.20, Y.24, L.40, P.119, R.120 Ligands: ACT.2 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Water bridges: B:N.96, C:R.20 Hydrogen bonds: C:Y.24 Salt bridges: C:R.20, C:R.120 SO4.5: 4 residues within 4Å: Chain A: S.2, H.3 Chain C: G.75, Y.76 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.76, A:H.3 Water bridges: C:K.70, C:D.77 SO4.6: 6 residues within 4Å: Chain A: H.3, A.5, A.6 Chain C: N.78, L.132, G.133 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.78, C:G.133, A:A.6 Water bridges: C:G.133 Salt bridges: A:H.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Digiovanni, S. et al., Two novel fish paralogs provide insights into the Rid family of imine deaminases active in pre-empting enamine/imine metabolic damage. Sci Rep (2020)

Release Date

2020-07-29

Peptides

Ribonuclease UK114: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Ribonuclease UK114

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