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

BON1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: S.268, E.271, K.272 Ligand excluded by PLIP EDO.2: 2 residues within 4Å: Chain A: N.39, L.46 Ligand excluded by PLIP EDO.3: 2 residues within 4Å: Chain A: D.105, K.107 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: L.351, R.356 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: D.50, V.72, L.74, V.104, D.105, T.106, F.108, Q.109 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: T.106, K.107 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: N.185, E.187, L.294, K.295, S.296 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: L.27, F.28, S.29, Y.89, F.91 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: K.48, D.50, N.75, T.106 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: K.58, V.94, Q.95, T.96 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: L.64, R.100 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: E.66, V.67, F.68, R.69 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: E.66, R.69, E.114 Ligands: PEG.12 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: E.126, K.147, R.148, K.149 Ligands: GOL.14, PGE.18 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: T.136, F.367, Y.368, D.369, S.370 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: R.140, E.169, K.174, E.313 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: F.392, N.393, G.396, N.419, V.420 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: T.11, A.14, L.15, Y.18, K.215 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.14, A:K.215 Water bridges: A:Y.18 GOL.14: 8 residues within 4Å: Chain A: K.58, L.64, V.98, R.100, E.126, T.128 Ligands: PGE.18, EDO.19 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.100, A:E.126, A:T.128, A:T.128 GOL.16: 7 residues within 4Å: Chain A: V.94, T.96, T.128, C.129, A.130, E.133, F.367 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.128, A:A.130 GOL.22: 5 residues within 4Å: Chain A: T.330, A.331, S.332, A.423, G.424 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.330, A:A.331, A:S.332

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

PEG.12: 7 residues within 4Å: Chain A: R.69, E.114, L.116, K.117, L.118, D.119 Ligands: EDO.17 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.69, A:E.114, A:L.118, A:D.119, A:D.119

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

PGE.18: 8 residues within 4Å: Chain A: E.126, A.127, T.128, T.143, L.144, E.145 Ligands: GOL.14, EDO.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.126, A:E.145

1 x CA: CALCIUM ION(Non-covalent)

CA.24: 3 residues within 4Å: Chain A: D.369, D.371, R.373 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.369, A:R.373

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
F

Protein BONZAI 1

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