SMTL ID : 6rms.1

The Structure of variant D274E of the Mo-insertase domain Cnx1E from Arabidopsis thaliana in complex with AMP

Coordinates

PDB Format Compare

Method

SOLUTION SCATTERING 1.74 Å

Oligo State

homo-dimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: K.279, P.280, G.281, R.354, M.384, S.385 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.281, A:S.385, A:S.385 Salt bridges: A:R.354 SO4.6: 6 residues within 4Å: Chain B: K.279, P.280, G.281, R.354, M.384, S.385 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.281, B:S.385, B:S.385 Salt bridges: B:R.354

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: V.32, G.151, E.152, R.153, G.331, W.332, T.333, S.334 Chain B: S.425 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.331, A:T.333, A:S.334, A:S.334 Water bridges: A:T.333 EDO.7: 9 residues within 4Å: Chain A: S.425 Chain B: V.32, G.151, E.152, R.153, G.331, W.332, T.333, S.334 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.331, B:T.333, B:S.334, B:S.334 Water bridges: B:T.333

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 5 residues within 4Å: Chain A: E.35, D.36, I.37, R.38, V.167 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.35 IMD.8: 5 residues within 4Å: Chain B: E.35, D.36, I.37, R.38, V.167 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.35

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 21 residues within 4Å: Chain A: S.182, T.183, E.186, L.187, I.200, R.201, D.202, S.203, N.204, R.205, S.250, G.251, G.252, V.253, G.309, N.310, P.311 Chain B: T.92, G.93, R.135 Ligands: MG.5 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.182, A:E.186, A:D.202, A:S.203, A:N.204, A:N.204, A:G.252, A:G.309 Water bridges: A:N.310, A:N.310, B:Y.46, B:G.93, B:R.135 AMP.9: 21 residues within 4Å: Chain A: T.92, G.93, R.135 Chain B: S.182, T.183, E.186, L.187, I.200, R.201, D.202, S.203, N.204, R.205, S.250, G.251, G.252, V.253, G.309, N.310, P.311 Ligands: MG.10 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Water bridges: A:Y.46, A:G.93, A:R.135, B:N.310, B:N.310 Hydrogen bonds: B:S.182, B:D.202, B:D.202, B:S.203, B:N.204, B:N.204, B:G.252, B:G.309

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: G.184, G.252 Ligands: AMP.4 6 PLIP interactions: 5 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.1, H2O.3, H2O.4, H2O.7, H2O.12, AMP.4 MG.10: 3 residues within 4Å: Chain B: G.184, G.252 Ligands: AMP.9 6 PLIP interactions: 5 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.3, H2O.10, H2O.11, H2O.12, H2O.16, AMP.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hercher, T.W. et al., Insights into the Cnx1E catalyzed MPT-AMP hydrolysis. Biosci.Rep. (2020)

Release Date

2020-02-19

Peptides

Molybdopterin biosynthesis protein CNX1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Molybdopterin biosynthesis protein CNX1