SMTL ID : 8std.3 (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 and soaked with CS2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: D.151, R.159 Ligands: DND.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.151, A:D.151 MG.3: 1 residues within 4Å: Ligands: DND.4 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain C: D.151, R.159 Ligands: DND.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.151, C:D.151 MG.7: 1 residues within 4Å: Ligands: DND.8 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain E: D.151, R.159 Ligands: DND.10 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.151, E:D.151 MG.11: 1 residues within 4Å: Ligands: DND.12 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain G: D.151, R.159 Ligands: DND.14 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.151, G:D.151 MG.15: 1 residues within 4Å: Ligands: DND.16 No protein-ligand interaction detected (PLIP)

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

DND.2: 29 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: E.50, V.51, I.52, Y.53, T.79, N.232, F.234 Chain H: C.221, A.222, S.223 Ligands: MG.1 17 PLIP interactions: 11 interactions with chain A, 5 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: A:A.124 Hydrogen bonds: A:G.125, A:T.126, A:A.127, A:D.128, A:V.154, A:G.178, A:G.181, A:A.182, A:L.183, A:Y.204, G:E.50, G:Y.53, G:T.79, H:S.223 pi-Stacking: G:Y.53, G:F.234 DND.4: 19 residues within 4Å: Chain B: A.124, G.125, T.126, A.127, D.128, G.153, V.154, A.177, G.178, M.179, E.180, G.181, A.182, L.183, T.200, V.202 Chain E: C.221 Chain F: Y.53 Ligands: MG.3 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:A.124, B:E.180, E:C.221 Hydrogen bonds: B:T.126, B:T.126, B:A.127, B:D.128, B:V.154, B:G.178, B:A.182, B:L.183 DND.6: 29 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: E.50, V.51, I.52, Y.53, T.79, N.232, F.234 Chain F: C.221, A.222, S.223 Ligands: MG.5 17 PLIP interactions: 11 interactions with chain C, 5 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: C:A.124 Hydrogen bonds: C:G.125, C:T.126, C:A.127, C:D.128, C:V.154, C:G.178, C:G.181, C:A.182, C:L.183, C:Y.204, E:E.50, E:Y.53, E:T.79, F:S.223 pi-Stacking: E:Y.53, E:F.234 DND.8: 19 residues within 4Å: Chain D: A.124, G.125, T.126, A.127, D.128, G.153, V.154, A.177, G.178, M.179, E.180, G.181, A.182, L.183, T.200, V.202 Chain G: C.221 Chain H: Y.53 Ligands: MG.7 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: D:A.124, D:E.180, G:C.221 Hydrogen bonds: D:T.126, D:T.126, D:A.127, D:D.128, D:V.154, D:G.178, D:A.182, D:L.183 DND.10: 29 residues within 4Å: Chain A: E.50, V.51, I.52, Y.53, T.79, N.232, F.234 Chain B: C.221, A.222, S.223 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.9 17 PLIP interactions: 5 interactions with chain A, 11 interactions with chain E, 1 interactions with chain B Hydrogen bonds: A:E.50, A:Y.53, A:T.79, E:G.125, E:T.126, E:A.127, E:D.128, E:V.154, E:G.178, E:G.181, E:A.182, E:L.183, E:Y.204, B:S.223 pi-Stacking: A:Y.53, A:F.234 Hydrophobic interactions: E:A.124 DND.12: 19 residues within 4Å: Chain C: C.221 Chain D: Y.53 Chain F: A.124, G.125, T.126, A.127, D.128, G.153, V.154, A.177, G.178, M.179, E.180, G.181, A.182, L.183, T.200, V.202 Ligands: MG.11 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain C Hydrophobic interactions: F:A.124, F:E.180, C:C.221 Hydrogen bonds: F:T.126, F:T.126, F:A.127, F:D.128, F:V.154, F:G.178, F:A.182, F:L.183 DND.14: 29 residues within 4Å: Chain C: E.50, V.51, I.52, Y.53, T.79, N.232, F.234 Chain D: C.221, A.222, S.223 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.13 17 PLIP interactions: 5 interactions with chain C, 11 interactions with chain G, 1 interactions with chain D Hydrogen bonds: C:E.50, C:Y.53, C:T.79, G:G.125, G:T.126, G:A.127, G:D.128, G:V.154, G:G.178, G:G.181, G:A.182, G:L.183, G:Y.204, D:S.223 pi-Stacking: C:Y.53, C:F.234 Hydrophobic interactions: G:A.124 DND.16: 19 residues within 4Å: Chain A: C.221 Chain B: Y.53 Chain H: A.124, G.125, T.126, A.127, D.128, G.153, V.154, A.177, G.178, M.179, E.180, G.181, A.182, L.183, T.200, V.202 Ligands: MG.15 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: H:A.124, H:E.180, A:C.221 Hydrogen bonds: H:T.126, 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
E

B
F

C
E

D
F

E
E

F
F

G
E

H
F

Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

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