SMTL ID : 6kxk.1 (7 other biounits)

BON1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 6 residues within 4Å: Chain A: Q.57, K.58, E.59, V.94, Q.95, T.96 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.59, A:T.96, A:T.96 Water bridges: A:E.59, A:T.96 PEG.2: 5 residues within 4Å: Chain A: E.66, V.67, F.68, R.69, K.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.66, A:K.83 Water bridges: A:K.83 PEG.7: 3 residues within 4Å: Chain A: R.182, V.300, D.301 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.273, A:V.300 PEG.11: 2 residues within 4Å: Chain A: R.182, F.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.182, A:R.182 PEG.25: 4 residues within 4Å: Chain A: L.74, N.75, Q.109 Ligands: EDO.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.75, A:Q.109, A:N.110

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

EDO.3: 4 residues within 4Å: Chain A: K.48, D.50, N.75, T.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.75, A:N.75 EDO.4: 4 residues within 4Å: Chain A: V.67, F.85, V.87, A.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.88 EDO.5: 9 residues within 4Å: Chain A: Y.89, H.90, T.93, V.94, Q.95, A.130, L.131, S.132 Ligands: EDO.17 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.90, A:Q.95, A:Q.95, A:L.131, A:S.132 EDO.6: 6 residues within 4Å: Chain A: T.11, F.198, K.215, T.216, V.218, H.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.216, A:H.257 EDO.8: 3 residues within 4Å: Chain A: Q.366, F.367, K.372 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: N.39, R.41, H.159, G.161, K.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.39, A:R.41, A:R.41, A:G.161 EDO.12: 2 residues within 4Å: Chain A: G.1, K.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.220 Water bridges: A:K.194 EDO.13: 3 residues within 4Å: Chain A: K.20, S.514, I.551 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.20, A:K.20 EDO.16: 2 residues within 4Å: Chain A: N.75 Ligands: PEG.25 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.74 EDO.17: 10 residues within 4Å: Chain A: Y.89, H.90, F.91, T.93, V.94, S.132, V.364, F.367, Y.368 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.90, A:S.132 EDO.19: 2 residues within 4Å: Chain A: N.281, K.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.281, A:K.295 EDO.23: 5 residues within 4Å: Chain A: T.330, A.331, S.332, A.423 Ligands: GOL.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.331, A:S.332, A:S.332

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: D.42, R.43, R.148, P.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.148 GOL.15: 4 residues within 4Å: Chain A: R.100, Y.102, F.123, E.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.102, A:E.126 Water bridges: A:R.100, A:L.118 GOL.18: 7 residues within 4Å: Chain A: K.58, A.62, L.64, V.98, R.100, E.126, T.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.62, A:R.100, A:E.126, A:T.128 GOL.20: 5 residues within 4Å: Chain A: R.373, Y.400, V.403, D.404, S.412 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.373, A:Y.400, A:Y.400, A:D.404, A:D.404, A:S.412 GOL.21: 6 residues within 4Å: Chain A: L.27, S.29, Y.89, F.91, F.311, P.542 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.29, A:Y.89, A:F.91 GOL.22: 1 residues within 4Å: Ligands: EDO.23 No protein-ligand interaction detected (PLIP)

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.14: 6 residues within 4Å: Chain A: R.69, E.114, L.116, K.117, L.118, D.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.69, A:L.118, A:D.119, A:D.119 PGE.24: 4 residues within 4Å: Chain A: T.128, T.143, L.144, E.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Q.C. et al., Crystal Structure of an Arabidopsis Copine providing insights into this protein family. To be published

Release Date

2020-09-16

Peptides

Protein BONZAI 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein BONZAI 1

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