SMTL ID : 6gbc.1

The Structure of variant R369A of the Mo-insertase domain Cnx1E from Arabidopsis thaliana in complex with AMP and molybdate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 22 residues within 4Å: Chain A: S.197, T.198, E.201, L.202, I.215, R.216, D.217, S.218, N.219, R.220, S.265, G.266, G.267, V.268, S.269, G.324, N.325, P.326 Chain B: T.107, G.108, R.150 Ligands: MG.2 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain A Water bridges: B:T.107, B:G.108, B:R.150, B:R.150 Hydrogen bonds: A:E.201, A:D.217, A:S.218, A:N.219, A:N.219, A:G.267, A:V.268, A:S.269, A:S.269, A:G.324 AMP.8: 22 residues within 4Å: Chain A: T.107, G.108, R.150 Chain B: S.197, T.198, E.201, L.202, I.215, R.216, D.217, S.218, N.219, R.220, S.265, G.266, G.267, V.268, S.269, G.324, N.325, P.326 Ligands: MG.9 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Water bridges: A:T.107, A:G.108, A:R.150, A:R.150 Hydrogen bonds: B:D.217, B:D.217, B:S.218, B:N.219, B:N.219, B:G.267, B:V.268, B:S.269, B:S.269, B:G.324

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: G.199, E.201, G.267 Ligands: AMP.1 6 PLIP interactions: 5 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.1, H2O.2, H2O.2, H2O.8, H2O.24, AMP.1 MG.9: 4 residues within 4Å: Chain B: G.199, E.201, G.267 Ligands: AMP.8 6 PLIP interactions: 1 Ligand-Ligand interactions, 5 Ligand-Water interactions Metal complexes: AMP.8, H2O.10, H2O.16, H2O.17, H2O.17, H2O.23

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

EDO.3: 9 residues within 4Å: Chain A: V.47, G.166, E.167, R.168, G.346, W.347, T.348, S.349 Chain B: S.440 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.346, A:T.348, A:S.349, A:S.349 Water bridges: A:T.348 EDO.4: 10 residues within 4Å: Chain A: G.170, A.171, S.172, E.173 Chain B: Q.229, L.330, M.406, S.408, A.409, S.434 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.171, A:S.172, B:S.408 Water bridges: A:S.172, A:S.172 EDO.5: 5 residues within 4Å: Chain A: I.37, E.50, M.184, V.185, K.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.50 EDO.6: 6 residues within 4Å: Chain A: Y.69, V.82, E.85, R.87, Y.104 Chain B: D.272 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.85, B:D.272 Water bridges: A:Y.69 EDO.10: 9 residues within 4Å: Chain A: S.440 Chain B: V.47, G.166, E.167, R.168, G.346, W.347, T.348, S.349 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.346, B:T.348, B:S.349, B:S.349 Water bridges: B:T.348 EDO.11: 10 residues within 4Å: Chain A: Q.229, L.330, M.406, S.408, A.409, S.434 Chain B: G.170, A.171, S.172, E.173 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.171, B:S.172, A:S.408 Water bridges: B:S.172, B:S.172 EDO.12: 5 residues within 4Å: Chain B: I.37, E.50, M.184, V.185, K.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.50 EDO.13: 6 residues within 4Å: Chain A: D.272 Chain B: Y.69, V.82, E.85, R.87, Y.104 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.69

2 x MOO: MOLYBDATE ION(Non-covalent)

MOO.7: 9 residues within 4Å: Chain A: K.294, P.295, G.296, K.297, P.298, P.323, N.325, S.328, S.400 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.296, A:K.297, A:N.325, A:S.328, A:S.400 Water bridges: A:S.400, A:S.400 MOO.14: 9 residues within 4Å: Chain B: K.294, P.295, G.296, K.297, P.298, P.323, N.325, S.328, S.400 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.296, B:K.297, B:N.325, B:S.328, B:S.400 Water bridges: B:S.400, B:S.400

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krausze, J. et al., The functional principle of eukaryotic molybdenum insertases. Biochem. J. (2018)

Release Date

2018-07-18

Peptides

Molybdopterin biosynthesis protein CNX1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Molybdopterin biosynthesis protein CNX1

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