SMTL ID : 7mj0.1 (2 other biounits)

LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with adenosine monophosphate AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

homo-octamer

Ligands

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 13 residues within 4Å: Chain A: T.126, S.127, Y.204 Chain G: V.51, Y.53, K.57, T.79, R.80, N.232, F.234 Chain H: C.221, S.223 Ligands: MG.3 7 PLIP interactions: 4 interactions with chain G, 2 interactions with chain A, 1 interactions with chain H Hydrogen bonds: G:V.51, G:Y.53, G:T.79, A:T.126, A:Y.204, H:S.223 Salt bridges: G:K.57 AMP.4: 13 residues within 4Å: Chain C: T.126, S.127, Y.204 Chain E: V.51, Y.53, K.57, T.79, R.80, N.232, F.234 Chain F: C.221, S.223 Ligands: MG.6 7 PLIP interactions: 2 interactions with chain C, 4 interactions with chain E, 1 interactions with chain F Hydrogen bonds: C:T.126, C:Y.204, E:V.51, E:Y.53, E:T.79, F:S.223 Salt bridges: E:K.57 AMP.7: 13 residues within 4Å: Chain A: V.51, Y.53, K.57, T.79, R.80, N.232, F.234 Chain B: C.221, S.223 Chain E: T.126, S.127, Y.204 Ligands: MG.9 7 PLIP interactions: 2 interactions with chain E, 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: E:T.126, E:Y.204, A:V.51, A:Y.53, A:T.79, B:S.223 Salt bridges: A:K.57 AMP.10: 13 residues within 4Å: Chain C: V.51, Y.53, K.57, T.79, R.80, N.232, F.234 Chain D: C.221, S.223 Chain G: T.126, S.127, Y.204 Ligands: MG.12 7 PLIP interactions: 2 interactions with chain G, 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: G:T.126, G:Y.204, C:V.51, C:Y.53, C:T.79, D:S.223 Salt bridges: C:K.57

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: G.188, V.191, K.193, S.223, G.224 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:G.188, A:V.191, A:S.223 MG.3: 5 residues within 4Å: Chain A: A.124, G.125, D.151, R.159 Ligands: AMP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.151, AMP.1 MG.5: 5 residues within 4Å: Chain C: G.188, V.191, K.193, S.223, G.224 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:G.188, C:V.191, C:S.223 MG.6: 5 residues within 4Å: Chain C: A.124, G.125, D.151, R.159 Ligands: AMP.4 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.151, AMP.4 MG.8: 5 residues within 4Å: Chain E: G.188, V.191, K.193, S.223, G.224 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:G.188, E:V.191, E:S.223 MG.9: 5 residues within 4Å: Chain E: A.124, G.125, D.151, R.159 Ligands: AMP.7 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:D.151, AMP.7 MG.11: 5 residues within 4Å: Chain G: G.188, V.191, K.193, S.223, G.224 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:G.188, G:V.191, G:S.223 MG.12: 5 residues within 4Å: Chain G: A.124, G.125, D.151, R.159 Ligands: AMP.10 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Ligand interactions Metal complexes: G:D.151, AMP.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rankin, J.A. et al., The LarB carboxylase/hydrolase forms a transient cysteinyl-pyridine intermediate during nickel-pincer nucleotide cofactor biosynthesis. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-09-29

Peptides

Pyridinium-3,5-biscarboxylic acid mononucleotide synthase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

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