SMTL ID : 6kxk.4 (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: 2 residues within 4Å: Chain A: L.64, R.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.100, A:R.100 Water bridges: A:L.64 PEG.11: 6 residues within 4Å: Chain A: R.69, E.114, L.116, K.117, L.118, D.119 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.69, A:K.117, A:L.118, A:D.119, A:D.119 PEG.14: 5 residues within 4Å: Chain A: R.140, E.168, E.169, K.174, E.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.169, A:K.174 Water bridges: A:R.140 PEG.17: 6 residues within 4Å: Chain A: G.349, L.351, Q.355, Q.407, M.410, T.414 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.349, A:Q.355, A:M.410 PEG.20: 6 residues within 4Å: Chain A: R.373, E.402, D.404, G.408, T.411, S.412 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.373, A:D.404, A:T.411

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: A.436, S.440, S.473, L.477 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.433, A:S.440, A:S.473 GOL.4: 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:A.331, A:S.332, A:S.332 GOL.9: 4 residues within 4Å: Chain A: E.66, V.67, F.68, R.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.69, A:R.69 GOL.10: 2 residues within 4Å: Chain A: R.100, Y.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.102, A:Y.102

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

EDO.3: 4 residues within 4Å: Chain A: N.433, D.469, A.470 Ligands: GOL.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.469 EDO.5: 5 residues within 4Å: Chain A: T.11, F.198, K.215, V.218, H.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.11, A:K.215, A:K.215 EDO.6: 3 residues within 4Å: Chain A: Y.17, K.20, S.514 No protein-ligand interaction detected (PLIP) EDO.7: 5 residues within 4Å: Chain A: Q.57, K.58, V.94, Q.95, T.96 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.96, A:T.96, A:T.96 EDO.8: 4 residues within 4Å: Chain A: K.58, L.64, R.100, E.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.100, A:E.126 EDO.12: 9 residues within 4Å: Chain A: Y.89, H.90, F.91, T.93, V.94, S.132, V.364, F.367, Y.368 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.90, A:S.132, A:V.364 Water bridges: A:Q.95, A:Q.95 EDO.15: 2 residues within 4Å: Chain A: F.192, S.193 No protein-ligand interaction detected (PLIP) EDO.16: 5 residues within 4Å: Chain A: L.15, D.16, L.19, E.217, K.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.217 EDO.18: 3 residues within 4Å: Chain A: R.350, L.351, R.356 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.351, A:R.356, A:R.356 EDO.19: 5 residues within 4Å: Chain A: K.60, D.360, E.363, V.364, S.532 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.60, A:D.360, A:E.363, A:E.363 EDO.21: 4 residues within 4Å: Chain A: G.405, I.406, Q.407 Ligands: PG4.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.406, A:Q.407 EDO.22: 6 residues within 4Å: Chain A: L.27, F.28, S.29, Y.89, H.90, F.91 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.29, A:F.91, A:E.92 EDO.23: 3 residues within 4Å: Chain A: E.126, K.147, K.149 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.149, A:K.149 Water bridges: A:E.126 EDO.24: 2 residues within 4Å: Chain A: N.110, S.111 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.13: 6 residues within 4Å: Chain A: T.96, A.130, Q.366, F.367, K.372 Ligands: EDO.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.96 Water bridges: A:A.130

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

CL.25: 4 residues within 4Å: Chain A: K.48, D.50, N.75, T.106 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.26: 4 residues within 4Å: Chain A: D.369, D.371, R.373, E.402 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.369, A:D.369, A:D.371, A:R.373, H2O.3

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
D

Protein BONZAI 1

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