SMTL ID : 6kxk.3 (7 other biounits)

BON1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: T.330, A.331, S.332, A.423 Ligands: GOL.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.331, A:S.332, A:S.332 EDO.4: 6 residues within 4Å: Chain A: Y.17, A.499, G.502, E.503, R.504, D.516 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.516 EDO.8: 3 residues within 4Å: Chain A: R.100, Y.102, F.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.102 EDO.9: 5 residues within 4Å: Chain A: V.263, K.265, I.280, N.281, S.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.283 EDO.10: 5 residues within 4Å: Chain A: S.341, L.342, N.352, A.353, R.356 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.342, A:A.353, A:D.525 EDO.11: 5 residues within 4Å: Chain A: L.394, G.396, S.415, A.416, N.419 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.415 EDO.13: 4 residues within 4Å: Chain A: D.498, D.500, K.501, F.520 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.500 EDO.14: 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.15: 3 residues within 4Å: Chain A: Q.57, K.58, V.94 No protein-ligand interaction detected (PLIP) EDO.16: 3 residues within 4Å: Chain A: K.58, E.59, T.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.58, A:K.58

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: L.74, N.75, Q.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.109, A:Q.109 GOL.7: 7 residues within 4Å: Chain A: G.26, F.28, S.29, Y.89, F.91, F.311, P.542 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.89, A:F.91 Water bridges: A:F.311 GOL.12: 6 residues within 4Å: Chain A: R.373, Y.400, E.402, V.403, D.404, G.408 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.373, A:Y.400, A:Y.400, A:D.404, A:D.404 GOL.18: 2 residues within 4Å: Chain A: R.382 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.382, A:R.382

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

PEG.3: 8 residues within 4Å: Chain A: T.11, N.12, F.198, K.215, T.216, V.218, H.257 Ligands: PGE.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.11, A:K.215, A:V.218 PEG.5: 5 residues within 4Å: Chain A: E.66, V.67, F.68, R.69, K.83 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.83, A:K.83 PEG.6: 6 residues within 4Å: Chain A: R.69, E.114, L.116, K.117, L.118, D.119 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.69, A:R.69, A:E.114, A:L.118, A:D.119, A:D.119

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

PGE.17: 8 residues within 4Å: Chain A: T.11, A.14, L.15, Y.18, P.212, V.213, K.215 Ligands: PEG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.11, A:P.212

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.19: 4 residues within 4Å: Chain A: K.48, D.50, N.75, T.106 Ligand excluded by PLIP

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
C

Protein BONZAI 1

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