SMTL ID : 4jhg.1

Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with trans-zeatin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x ZEA: (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol(Non-covalent)

ZEA.1: 17 residues within 4Å: Chain A: T.71, Q.73, Y.87, V.89, I.103, F.105, Y.125, Y.138, A.141, G.142, R.145, F.146, F.149 Chain B: V.65, G.66, D.67, F.68 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.67, A:Q.73, A:Y.87, A:Y.138 pi-Stacking: A:F.105 ZEA.6: 17 residues within 4Å: Chain A: V.65, G.66, D.67, F.68 Chain B: T.71, Q.73, Y.87, V.89, I.103, F.105, Y.125, Y.138, A.141, G.142, R.145, F.146, F.149 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.67, B:Q.73, B:Y.87, B:Y.87, B:Y.138 pi-Stacking: B:F.105

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 4 residues within 4Å: Chain A: E.91, G.92, I.93, A.94 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.92, A:I.93, A:A.94 MLI.7: 4 residues within 4Å: Chain B: E.91, G.92, I.93, A.94 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.92, B:I.93, B:A.94

6 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: F.64, V.65, G.66 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:G.66, A:G.69 Hydrogen bonds: B:A.94 NA.4: 3 residues within 4Å: Chain A: S.70, T.71 Chain B: D.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.70, A:S.70 NA.5: 3 residues within 4Å: Chain A: F.4, T.5, G.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.5, A:G.129, A:G.129 NA.8: 3 residues within 4Å: Chain B: F.64, V.65, G.66 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:G.66, B:G.69 Hydrogen bonds: A:A.94 NA.9: 3 residues within 4Å: Chain A: D.67 Chain B: S.70, T.71 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.70, B:T.71, B:T.71 NA.10: 3 residues within 4Å: Chain B: F.4, T.5, G.129 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.5, B:G.129, B:G.129 Water bridges: B:D.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruszkowski, M. et al., The landscape of cytokinin binding by a plant nodulin. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-03-20

Peptides

MtN13 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

MtN13 protein

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