SMTL ID : 8soq.2 (2 other biounits)

S127A variant of LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with authentic substrate NaAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-octamer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.151, R.159 Ligands: DND.2 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain B: D.151, R.159 Ligands: DND.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.151, B:D.151 MG.4: 6 residues within 4Å: Chain B: G.188, V.191, K.193, V.195, S.223, G.224 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:K.193 MG.6: 3 residues within 4Å: Chain C: D.151, R.159 Ligands: DND.7 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: D.151, R.159 Ligands: DND.10 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.151, D:D.151 MG.9: 6 residues within 4Å: Chain D: G.188, V.191, K.193, V.195, S.223, G.224 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:K.193 MG.11: 3 residues within 4Å: Chain E: D.151, R.159 Ligands: DND.12 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain F: D.151, R.159 Ligands: DND.15 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.151, F:D.151 MG.14: 6 residues within 4Å: Chain F: G.188, V.191, K.193, V.195, S.223, G.224 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:K.193 MG.16: 3 residues within 4Å: Chain G: D.151, R.159 Ligands: DND.17 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain H: D.151, R.159 Ligands: DND.20 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.151, H:D.151 MG.19: 6 residues within 4Å: Chain H: G.188, V.191, K.193, V.195, S.223, G.224 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:K.193

8 x DND: NICOTINIC ACID ADENINE DINUCLEOTIDE(Non-covalent)

DND.2: 25 residues within 4Å: Chain A: A.124, G.125, T.126, A.127, D.128, D.151, G.153, V.154, A.155, A.177, G.178, M.179, E.180, G.181, A.182, L.183, V.202, Y.204 Chain G: V.51, Y.53, T.79, R.80 Chain H: C.221, A.222 Ligands: MG.1 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain G Hydrophobic interactions: A:A.124 Hydrogen bonds: A:T.126, A:A.127, A:D.128, A:V.154, A:G.178, A:M.179, A:G.181, A:A.182, A:L.183, A:Y.204, G:Y.53, G:T.79 pi-Stacking: G:Y.53, G:Y.53, G:F.234 DND.5: 20 residues within 4Å: Chain B: A.124, G.125, T.126, A.127, D.128, D.151, G.153, V.154, A.177, G.178, M.179, E.180, G.181, A.182, L.183, V.202 Chain E: S.220, C.221 Chain F: R.80 Ligands: MG.3 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:A.124, B:V.154, E:C.221 Hydrogen bonds: B:T.126, B:A.127, B:D.128, B:V.154, B:G.178, B:A.182, B:L.183 DND.7: 25 residues within 4Å: Chain C: A.124, G.125, T.126, A.127, D.128, D.151, G.153, V.154, A.155, A.177, G.178, M.179, E.180, G.181, A.182, L.183, V.202, Y.204 Chain E: V.51, Y.53, T.79, R.80 Chain F: C.221, A.222 Ligands: MG.6 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain E Hydrophobic interactions: C:A.124 Hydrogen bonds: C:T.126, C:A.127, C:D.128, C:V.154, C:G.178, C:M.179, C:G.181, C:A.182, C:L.183, C:Y.204, E:Y.53, E:T.79 pi-Stacking: E:Y.53, E:Y.53, E:F.234 DND.10: 20 residues within 4Å: Chain D: A.124, G.125, T.126, A.127, D.128, D.151, G.153, V.154, A.177, G.178, M.179, E.180, G.181, A.182, L.183, V.202 Chain G: S.220, C.221 Chain H: R.80 Ligands: MG.8 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: D:A.124, D:V.154, G:C.221 Hydrogen bonds: D:T.126, D:A.127, D:D.128, D:V.154, D:G.178, D:A.182, D:L.183 DND.12: 25 residues within 4Å: Chain A: V.51, Y.53, T.79, R.80 Chain B: C.221, A.222 Chain E: A.124, G.125, T.126, A.127, D.128, D.151, G.153, V.154, A.155, A.177, G.178, M.179, E.180, G.181, A.182, L.183, V.202, Y.204 Ligands: MG.11 16 PLIP interactions: 11 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: E:A.124 Hydrogen bonds: E:T.126, E:A.127, E:D.128, E:V.154, E:G.178, E:M.179, E:G.181, E:A.182, E:L.183, E:Y.204, A:Y.53, A:T.79 pi-Stacking: A:Y.53, A:Y.53, A:F.234 DND.15: 20 residues within 4Å: Chain C: S.220, C.221 Chain D: R.80 Chain F: A.124, G.125, T.126, A.127, D.128, D.151, G.153, V.154, A.177, G.178, M.179, E.180, G.181, A.182, L.183, V.202 Ligands: MG.13 10 PLIP interactions: 1 interactions with chain C, 9 interactions with chain F Hydrophobic interactions: C:C.221, F:A.124, F:V.154 Hydrogen bonds: F:T.126, F:A.127, F:D.128, F:V.154, F:G.178, F:A.182, F:L.183 DND.17: 25 residues within 4Å: Chain C: V.51, Y.53, T.79, R.80 Chain D: C.221, A.222 Chain G: A.124, G.125, T.126, A.127, D.128, D.151, G.153, V.154, A.155, A.177, G.178, M.179, E.180, G.181, A.182, L.183, V.202, Y.204 Ligands: MG.16 16 PLIP interactions: 11 interactions with chain G, 5 interactions with chain C Hydrophobic interactions: G:A.124 Hydrogen bonds: G:T.126, G:A.127, G:D.128, G:V.154, G:G.178, G:M.179, G:G.181, G:A.182, G:L.183, G:Y.204, C:Y.53, C:T.79 pi-Stacking: C:Y.53, C:Y.53, C:F.234 DND.20: 20 residues within 4Å: Chain A: S.220, C.221 Chain B: R.80 Chain H: A.124, G.125, T.126, A.127, D.128, D.151, G.153, V.154, A.177, G.178, M.179, E.180, G.181, A.182, L.183, V.202 Ligands: MG.18 10 PLIP interactions: 9 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: H:A.124, H:V.154, A:C.221 Hydrogen bonds: H:T.126, H:A.127, H:D.128, H:V.154, H:G.178, H:A.182, H:L.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chatterjee, S. et al., Structure of the LarB-Substrate Complex and Identification of a Reaction Intermediate during Nickel-Pincer Nucleotide Cofactor Biosynthesis. Biochemistry (2023)

Release Date

2023-12-27

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
C

D
D

E
C

F
D

G
C

H
D

Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

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