SMTL ID : 6eth.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 23 residues within 4Å: Chain A: S.202, T.203, E.206, L.207, I.220, R.221, D.222, S.223, N.224, R.225, S.270, G.271, G.272, V.273, S.274, G.329, N.330, P.331 Chain B: T.112, G.113, R.155 Ligands: MG.2, ACE.15 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain A Water bridges: B:T.112, B:G.113, B:G.113, B:R.155, A:E.206, A:E.206 Hydrogen bonds: A:E.206, A:D.222, A:S.223, A:N.224, A:N.224, A:G.272, A:S.274, A:G.329 AMP.9: 23 residues within 4Å: Chain A: T.112, G.113, R.155 Chain B: S.202, T.203, E.206, L.207, I.220, R.221, D.222, S.223, N.224, R.225, S.270, G.271, G.272, V.273, S.274, G.329, N.330, P.331 Ligands: ACE.7, MG.10 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Water bridges: A:T.112, A:G.113, A:G.113, A:R.155, B:E.206, B:E.206 Hydrogen bonds: B:D.222, B:D.222, B:S.223, B:N.224, B:N.224, B:G.272, B:S.274, B:G.329

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: G.204, E.206, G.272 Ligands: AMP.1, ACE.15 6 PLIP interactions: 5 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.1, H2O.2, H2O.5, H2O.7, H2O.17, AMP.1 MG.10: 5 residues within 4Å: Chain B: G.204, E.206, G.272 Ligands: ACE.7, AMP.9 6 PLIP interactions: 5 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.5, H2O.13, H2O.14, H2O.17, H2O.20, AMP.9

2 x WO4: TUNGSTATE(VI)ION(Non-covalent)

WO4.3: 7 residues within 4Å: Chain A: K.299, P.300, G.301, K.302, S.333, R.374, S.405 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.301, A:K.302, A:R.374, A:R.374, A:S.405 Water bridges: A:K.299, A:S.333, A:S.333, A:S.405 WO4.11: 7 residues within 4Å: Chain B: K.299, P.300, G.301, K.302, S.333, R.374, S.405 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.301, B:K.302, B:R.374, B:R.374, B:S.405 Water bridges: B:K.299, B:S.333, B:S.333, B:S.405

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

EDO.4: 9 residues within 4Å: Chain A: V.52, G.171, E.172, R.173, G.351, W.352, T.353, S.354 Chain B: S.445 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.353, A:T.353, A:S.354, A:S.354 Water bridges: A:T.353 EDO.5: 10 residues within 4Å: Chain A: G.175, A.176, S.177, E.178 Chain B: M.411, R.412, S.413, A.414, N.415, S.439 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.177, A:S.177, B:S.413, B:S.439 Water bridges: A:A.176, B:A.414, B:A.414 EDO.6: 7 residues within 4Å: Chain A: D.277 Chain B: Y.74, V.87, E.90, R.92, Y.109, K.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.277 EDO.12: 9 residues within 4Å: Chain A: S.445 Chain B: V.52, G.171, E.172, R.173, G.351, W.352, T.353, S.354 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.353, B:T.353, B:S.354, B:S.354 Water bridges: B:T.353 EDO.13: 10 residues within 4Å: Chain A: M.411, R.412, S.413, A.414, N.415, S.439 Chain B: G.175, A.176, S.177, E.178 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.413, A:S.439, B:S.177, B:S.177 Water bridges: A:A.414, A:A.414, B:A.176 EDO.14: 7 residues within 4Å: Chain A: Y.74, V.87, E.90, R.92, Y.109, K.140 Chain B: D.277 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.90, B:D.277, B:D.277

4 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.7: 9 residues within 4Å: Chain A: R.92, A.93, T.111, T.112, G.113, G.114 Chain B: E.206 Ligands: AMP.9, MG.10 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.111, A:T.112 ACE.8: 8 residues within 4Å: Chain A: E.366, P.367, I.368, K.369, H.378, S.399, G.401, Q.403 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.401 ACE.15: 9 residues within 4Å: Chain A: E.206 Chain B: R.92, A.93, T.111, T.112, G.113, G.114 Ligands: AMP.1, MG.2 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.111, B:T.112 ACE.16: 8 residues within 4Å: Chain B: E.366, P.367, I.368, K.369, H.378, S.399, G.401, Q.403 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.401

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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