SMTL ID : 4gy9.2 (1 other biounit)

Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with N6-isopentenyladenine (2iP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-tetramer

Ligands

4 x ZIP: N-(3-METHYLBUT-2-EN-1-YL)-9H-PURIN-6-AMINE(Non-covalent)

ZIP.1: 9 residues within 4Å: Chain A: T.71, Q.73, Y.87, V.89, F.105, A.141, G.142, R.145, F.149 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.73, A:Y.87 pi-Stacking: A:F.105 ZIP.9: 9 residues within 4Å: Chain B: T.71, Q.73, Y.87, V.89, F.105, A.141, G.142, R.145, F.149 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.73, B:Y.87 pi-Stacking: B:F.105 ZIP.17: 9 residues within 4Å: Chain C: T.71, Q.73, Y.87, V.89, F.105, A.141, G.142, R.145, F.149 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.73, C:Y.87, C:Y.87 pi-Stacking: C:F.105 ZIP.25: 9 residues within 4Å: Chain D: T.71, Q.73, Y.87, V.89, F.105, A.141, G.142, R.145, F.149 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.73, D:Y.87, D:Y.87 pi-Stacking: D:F.105

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

NA.2: 2 residues within 4Å: Chain A: S.70, T.71 Ligand excluded by PLIP NA.3: 3 residues within 4Å: Chain A: F.64, V.65, G.66 Ligand excluded by PLIP NA.4: 1 residues within 4Å: Chain A: A.39 Ligand excluded by PLIP NA.5: 2 residues within 4Å: Chain A: T.5, G.129 Ligand excluded by PLIP NA.6: 1 residues within 4Å: Chain A: S.70 Ligand excluded by PLIP NA.7: 3 residues within 4Å: Chain A: T.112, E.115, G.116 Ligand excluded by PLIP NA.10: 2 residues within 4Å: Chain B: S.70, T.71 Ligand excluded by PLIP NA.11: 3 residues within 4Å: Chain B: F.64, V.65, G.66 Ligand excluded by PLIP NA.12: 1 residues within 4Å: Chain B: A.39 Ligand excluded by PLIP NA.13: 2 residues within 4Å: Chain B: T.5, G.129 Ligand excluded by PLIP NA.14: 1 residues within 4Å: Chain B: S.70 Ligand excluded by PLIP NA.15: 3 residues within 4Å: Chain B: T.112, E.115, G.116 Ligand excluded by PLIP NA.18: 2 residues within 4Å: Chain C: S.70, T.71 Ligand excluded by PLIP NA.19: 3 residues within 4Å: Chain C: F.64, V.65, G.66 Ligand excluded by PLIP NA.20: 1 residues within 4Å: Chain C: A.39 Ligand excluded by PLIP NA.21: 2 residues within 4Å: Chain C: T.5, G.129 Ligand excluded by PLIP NA.22: 1 residues within 4Å: Chain C: S.70 Ligand excluded by PLIP NA.23: 3 residues within 4Å: Chain C: T.112, E.115, G.116 Ligand excluded by PLIP NA.26: 2 residues within 4Å: Chain D: S.70, T.71 Ligand excluded by PLIP NA.27: 3 residues within 4Å: Chain D: F.64, V.65, G.66 Ligand excluded by PLIP NA.28: 1 residues within 4Å: Chain D: A.39 Ligand excluded by PLIP NA.29: 2 residues within 4Å: Chain D: T.5, G.129 Ligand excluded by PLIP NA.30: 1 residues within 4Å: Chain D: S.70 Ligand excluded by PLIP NA.31: 3 residues within 4Å: Chain D: T.112, E.115, G.116 Ligand excluded by PLIP

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

MLI.8: 4 residues within 4Å: Chain A: E.91, G.92, I.93, A.94 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.91, A:G.92, A:I.93, A:A.94 MLI.16: 4 residues within 4Å: Chain B: E.91, G.92, I.93, A.94 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.91, B:G.92, B:I.93, B:A.94 MLI.24: 4 residues within 4Å: Chain C: E.91, G.92, I.93, A.94 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.92, C:I.93, C:A.94 MLI.32: 4 residues within 4Å: Chain D: E.91, G.92, I.93, A.94 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.92, D:I.93, D:A.94

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

2013-09-04

Peptides

MtN13 protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

MtN13 protein

Related Entries With Identical Sequence