- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.10 Å
- Oligo State
- homo-octamer
- Ligands
- 12 x MG: MAGNESIUM ION(Non-covalent)
- 8 x DND: NICOTINIC ACID ADENINE DINUCLEOTIDE(Non-covalent)
DND.3: 24 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
- Chain H: C.221, S.223
- Ligands: MG.1
11 PLIP interactions:9 interactions with chain A, 2 interactions with chain G- Hydrogen bonds: 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:Y.53, G:T.79
DND.5: 18 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, A.182, L.183, V.202
- Chain E: S.220, C.221
- Chain F: N.232
- Ligands: MG.4
10 PLIP interactions:9 interactions with chain B, 1 interactions with chain F- Hydrophobic interactions: B:A.124
- Hydrogen bonds: B:T.126, B:A.127, B:D.128, B:V.154, B:G.178, B:E.180, B:A.182, B:L.183
- Salt bridges: F:K.57
DND.8: 24 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
- Chain F: C.221, S.223
- Ligands: MG.6
11 PLIP interactions:9 interactions with chain C, 2 interactions with chain E- Hydrogen bonds: 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:Y.53, E:T.79
DND.10: 18 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, A.182, L.183, V.202
- Chain G: S.220, C.221
- Chain H: N.232
- Ligands: MG.9
10 PLIP interactions:9 interactions with chain D, 1 interactions with chain H- Hydrophobic interactions: D:A.124
- Hydrogen bonds: D:T.126, D:A.127, D:D.128, D:V.154, D:G.178, D:E.180, D:A.182, D:L.183
- Salt bridges: H:K.57
DND.13: 24 residues within 4Å:- Chain A: V.51, Y.53, T.79
- Chain B: C.221, 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.11
11 PLIP interactions:9 interactions with chain E, 2 interactions with chain A- Hydrogen bonds: 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, A:Y.53, A:T.79
DND.15: 18 residues within 4Å:- Chain C: S.220, C.221
- Chain D: N.232
- Chain F: A.124, G.125, T.126, A.127, D.128, G.153, V.154, A.177, G.178, M.179, E.180, A.182, L.183, V.202
- Ligands: MG.14
10 PLIP interactions:9 interactions with chain F, 1 interactions with chain D- Hydrophobic interactions: F:A.124
- Hydrogen bonds: F:T.126, F:A.127, F:D.128, F:V.154, F:G.178, F:E.180, F:A.182, F:L.183
- Salt bridges: D:K.57
DND.18: 24 residues within 4Å:- Chain C: V.51, Y.53, T.79
- Chain D: C.221, 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.16
11 PLIP interactions:9 interactions with chain G, 2 interactions with chain C- Hydrogen bonds: 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, C:Y.53, C:T.79
DND.20: 18 residues within 4Å:- Chain A: S.220, C.221
- Chain B: N.232
- Chain H: A.124, G.125, T.126, A.127, D.128, G.153, V.154, A.177, G.178, M.179, E.180, A.182, L.183, V.202
- Ligands: MG.19
10 PLIP interactions:9 interactions with chain H, 1 interactions with chain B- Hydrophobic interactions: H:A.124
- Hydrogen bonds: H:T.126, H:A.127, H:D.128, H:V.154, H:G.178, H:E.180, H:A.182, H:L.183
- Salt bridges: B:K.57
- 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
AB
BC
AD
BE
AF
BG
AH
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.10 Å
- Oligo State
- homo-octamer
- Ligands
- 12 x MG: MAGNESIUM ION(Non-covalent)
- 8 x DND: NICOTINIC ACID ADENINE DINUCLEOTIDE(Non-covalent)
- 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
AB
BC
AD
BE
AF
BG
AH
B