- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.65 Å
- Oligo State
- homo-octamer
- Ligands
- 12 x MG: MAGNESIUM ION(Non-covalent)
- 8 x DND: NICOTINIC ACID ADENINE DINUCLEOTIDE(Non-covalent)
DND.3: 27 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, K.57, T.79, R.80, N.232, F.234
- Chain H: A.222
- Ligands: MG.2
16 PLIP interactions:5 interactions with chain G, 11 interactions with chain A- Hydrogen bonds: G:Y.53, G:T.79, A:T.126, A:D.128, A:V.154, A:G.178, A:G.181, A:A.182, A:L.183, A:Y.204
- Salt bridges: G:K.57, G:K.57
- pi-Stacking: G:F.234
- Hydrophobic interactions: A:A.124, A:A.155, A:E.180
DND.5: 19 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, T.200, V.202
- Chain E: C.221
- Chain F: Y.53
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.8: 27 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, K.57, T.79, R.80, N.232, F.234
- Chain F: A.222
- Ligands: MG.7
16 PLIP interactions:11 interactions with chain C, 5 interactions with chain E- Hydrophobic interactions: C:A.124, C:A.155, C:E.180
- Hydrogen bonds: C:T.126, 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
- Salt bridges: E:K.57, E:K.57
- pi-Stacking: E:F.234
DND.10: 19 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, T.200, V.202
- Chain G: C.221
- Chain H: Y.53
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.13: 27 residues within 4Å:- Chain A: V.51, Y.53, K.57, T.79, R.80, N.232, F.234
- Chain B: 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.12
16 PLIP interactions:11 interactions with chain E, 5 interactions with chain A- Hydrophobic interactions: E:A.124, E:A.155, E:E.180
- Hydrogen bonds: E:T.126, 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
- Salt bridges: A:K.57, A:K.57
- pi-Stacking: A:F.234
DND.15: 19 residues within 4Å:- Chain C: C.221
- Chain D: Y.53
- 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, T.200, V.202
11 PLIP interactions:1 interactions with chain C, 10 interactions with chain F- Hydrophobic interactions: C:C.221, F:A.124, F:E.180
- 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.18: 27 residues within 4Å:- Chain C: V.51, Y.53, K.57, T.79, R.80, N.232, F.234
- Chain D: 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.17
16 PLIP interactions:5 interactions with chain C, 11 interactions with chain G- Hydrogen bonds: C:Y.53, C:T.79, G:T.126, G:D.128, G:V.154, G:G.178, G:G.181, G:A.182, G:L.183, G:Y.204
- Salt bridges: C:K.57, C:K.57
- pi-Stacking: C:F.234
- Hydrophobic interactions: G:A.124, G:A.155, G:E.180
DND.20: 19 residues within 4Å:- Chain A: C.221
- Chain B: Y.53
- 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, T.200, V.202
11 PLIP interactions:1 interactions with chain A, 10 interactions with chain H- Hydrophobic interactions: A:C.221, H:A.124, H:E.180
- 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
CB
DC
CD
DE
CF
DG
CH
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.65 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
CB
DC
CD
DE
CF
DG
CH
D