SMTL ID : 5dnu.1

Crystal structure of Striga KAI2-like protein in complex with karrikin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x KKN: 3-methyl-2H-furo[2,3-c]pyran-2-one(Non-covalent)

KKN.1: 12 residues within 4Å: Chain A: F.31, S.100, L.101, F.129, L.147, F.162, V.166, F.195, I.198, F.199, A.224, H.251 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.31, A:F.129, A:L.147, A:F.162, A:F.195, A:I.198 Water bridges: A:F.31 pi-Stacking: A:H.251

9 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 6 residues within 4Å: Chain A: Y.49, I.95, Q.118, I.269, K.270 Ligands: NA.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.118 FMT.3: 5 residues within 4Å: Chain A: D.134, Y.135, R.204, Y.232, R.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.134, A:R.204, A:Y.232 FMT.4: 3 residues within 4Å: Chain A: F.69, E.70, R.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.71, A:R.71 FMT.5: 6 residues within 4Å: Chain A: P.114, F.117, Q.118, V.212, P.213 Ligands: EDO.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.114 FMT.6: 2 residues within 4Å: Chain A: E.70, S.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.70, A:S.73 FMT.7: 3 residues within 4Å: Chain A: P.263, V.264, R.267 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.267 FMT.8: 1 residues within 4Å: Chain A: R.209 No protein-ligand interaction detected (PLIP) FMT.9: 2 residues within 4Å: Chain A: G.19, S.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.20 Water bridges: A:G.19 FMT.10: 5 residues within 4Å: Chain A: H.215, R.267, H.268, N.271, D.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.267 Water bridges: A:R.267

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

NA.11: 7 residues within 4Å: Chain A: Q.118, K.119, I.269, K.270, N.271, D.272 Ligands: FMT.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.118, A:K.119, A:K.270, A:D.272 NA.12: 4 residues within 4Å: Chain A: V.9, R.13, V.84, E.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.13, A:R.13, A:E.88 NA.13: 5 residues within 4Å: Chain A: H.68, F.69, E.70, Y.72, S.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.68

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

EDO.14: 1 residues within 4Å: Chain A: P.43 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.43 EDO.15: 3 residues within 4Å: Chain A: Y.232, N.235, R.236 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.235, A:R.236 EDO.16: 1 residues within 4Å: Chain A: H.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.87 EDO.17: 5 residues within 4Å: Chain A: P.114, T.211, V.212, P.213 Ligands: FMT.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.211, A:T.211 EDO.18: 5 residues within 4Å: Chain A: Y.135, L.136, S.228, V.229, Y.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.136 Water bridges: A:D.134

1 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.19: 5 residues within 4Å: Chain A: Q.76, H.80, I.108, I.112, Y.206 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.76, A:H.80, A:I.108, A:I.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y. et al., Structural basis of unique ligand specificity of KAI2-like protein from parasitic weed Striga hermonthica. Sci Rep (2016)

Release Date

2016-08-17

Peptides

ShKAI2iB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ShKAI2iB

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