SMTL ID : 6pt8.1

Crystal Structure of CobT from Methanocaldococcus jannaschii in complex with Adenine Alpha-Ribotide and Nicotinic Acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x AAM: ALPHA-ADENOSINE MONOPHOSPHATE(Non-covalent)

AAM.1: 27 residues within 4Å: Chain A: S.38, G.39, V.40, T.48, D.52, P.68, I.69, D.70, T.76, P.77, E.150, S.151, V.152, P.153, G.154, G.155, T.156, T.157, S.176, G.177, K.186, Q.241, V.313, E.315, G.316, V.317 Ligands: NIO.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.38, A:S.38, A:G.39, A:E.150, A:V.152, A:V.152, A:G.154, A:T.156, A:T.156, A:G.177, A:G.177, A:V.317 Water bridges: A:I.37, A:T.156, A:T.156, A:T.157 Salt bridges: A:K.186 AAM.5: 27 residues within 4Å: Chain B: S.38, G.39, V.40, T.48, D.52, P.68, I.69, D.70, T.76, P.77, E.150, S.151, V.152, P.153, G.154, G.155, T.156, T.157, S.176, G.177, K.186, Q.241, V.313, E.315, G.316, V.317 Ligands: NIO.4 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:S.38, B:S.38, B:G.39, B:E.150, B:S.151, B:V.152, B:G.154, B:T.156, B:T.156, B:G.177, B:G.177, B:V.317 Water bridges: B:I.37, B:K.186, B:K.186, B:K.186 Salt bridges: B:K.186

2 x NIO: NICOTINIC ACID(Non-covalent)

NIO.2: 14 residues within 4Å: Chain A: E.150, T.156, S.175, S.176, G.177, G.239, T.240, Q.241, V.270, V.313, K.314, E.315, G.316 Ligands: AAM.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.156, A:K.314 Hydrogen bonds: A:G.239, A:T.240, A:T.240, A:Q.241, A:Q.241 NIO.4: 14 residues within 4Å: Chain B: E.150, T.156, S.175, S.176, G.177, G.239, T.240, Q.241, V.270, V.313, K.314, E.315, G.316 Ligands: AAM.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.156 Hydrogen bonds: B:S.175, B:G.239, B:T.240, B:T.240, B:Q.241

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 3 residues within 4Å: Chain A: R.230, K.232 Chain B: K.91 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:K.91 Salt bridges: B:K.91, A:R.230, A:K.232 PO4.6: 4 residues within 4Å: Chain A: K.91 Chain B: D.142, R.230, K.232 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:K.91, B:R.230, B:K.232 Water bridges: B:K.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeter, V.L. et al., Structural studies of the phosphoribosyltransferase involved in cobamide biosynthesis in methanogenic archaea and cyanobacteria. Sci Rep (2022)

Release Date

2020-07-22

Peptides

UPF0284 protein MJ1598: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

UPF0284 protein MJ1598

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