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

Crystal structure of yellow lupin LLPR-10.1A protein in complex with trans-zeatin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

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

ZEA.1: 16 residues within 4Å: Chain A: N.7, Q.9, Y.19, L.22, T.23, Y.80, Y.82, S.101, I.103, G.113, K.114, I.115, G.138, L.139, F.142 Ligands: ZEA.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.22, A:L.22, A:Y.80, A:Y.82 Hydrogen bonds: A:N.7, A:S.101 Water bridges: A:F.142 ZEA.2: 10 residues within 4Å: Chain A: F.5, N.7, Y.99, V.117, F.119, R.131, D.132, A.134, K.135 Ligands: ZEA.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.5, A:R.131, A:K.135 Hydrogen bonds: A:Y.99, A:R.131, A:K.135 Water bridges: A:N.7, A:D.132, A:K.135, A:G.138, A:G.138 ZEA.3: 12 residues within 4Å: Chain A: S.26, D.27, V.30, K.53, I.55, V.66, H.68, Y.82, I.84, Y.99, G.138, L.141 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.30, A:I.55 Hydrogen bonds: A:K.53, A:Y.80, A:Y.99 Water bridges: A:S.26, A:H.68, A:H.68, A:G.138 ZEA.4: 3 residues within 4Å: Chain A: H.62, T.63, E.88 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.62 Hydrogen bonds: A:T.63, A:T.63, A:E.88 pi-Stacking: A:H.62, A:H.62 ZEA.5: 10 residues within 4Å: Chain A: V.33, I.34, G.140, K.143, A.144 Chain B: V.33, I.34, G.140, A.144 Ligands: ZEA.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.34 Water bridges: A:F.136 ZEA.7: 16 residues within 4Å: Chain B: N.7, Q.9, Y.19, L.22, T.23, Y.80, Y.82, S.101, I.103, G.113, K.114, I.115, G.138, L.139, F.142 Ligands: ZEA.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.22, B:L.22, B:Y.80, B:Y.82 Hydrogen bonds: B:N.7, B:S.101 Water bridges: B:F.142 ZEA.8: 10 residues within 4Å: Chain B: F.5, N.7, Y.99, V.117, F.119, R.131, D.132, A.134, K.135 Ligands: ZEA.7 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.5, B:R.131, B:K.135 Hydrogen bonds: B:R.131, B:K.135 Water bridges: B:N.7, B:D.132, B:K.135, B:G.138, B:G.138 ZEA.9: 12 residues within 4Å: Chain B: S.26, D.27, V.30, K.53, I.55, V.66, H.68, Y.82, I.84, Y.99, G.138, L.141 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.30, B:I.55 Hydrogen bonds: B:K.53, B:Y.99, B:Y.99 Water bridges: B:S.26, B:H.68, B:Y.80, B:G.138 ZEA.10: 3 residues within 4Å: Chain B: H.62, T.63, E.88 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:H.62 Hydrogen bonds: B:T.63, B:E.88 pi-Stacking: B:H.62, B:H.62 ZEA.11: 10 residues within 4Å: Chain A: V.33, I.34, G.140, A.144 Chain B: V.33, I.34, G.140, K.143, A.144 Ligands: ZEA.5 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.34 Water bridges: B:F.136

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

SO4.6: 6 residues within 4Å: Chain A: N.7, Q.9, L.139 Chain B: K.135, F.136 Ligands: SO4.12 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.7, A:Q.9 Salt bridges: A:K.135, B:K.135 Water bridges: B:K.135 SO4.12: 6 residues within 4Å: Chain A: K.135, F.136 Chain B: N.7, Q.9, L.139 Ligands: SO4.6 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.7, B:Q.9 Salt bridges: B:K.135, A:K.135 Water bridges: A:K.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sliwiak, J. et al., Crystallographic and CD probing of ligand-induced conformational changes in a plant PR-10 protein. J.Struct.Biol. (2016)

Release Date

2015-12-09

Peptides

Protein LLPR-10.1A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protein LLPR-10.1A

Related Entries With Identical Sequence