SMTL ID : 5ow3.1

Crystal structure of a C-terminally truncated trimeric ectodomain of the Arabidopsis thaliana gamete fusion protein HAP2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-trimer

Ligands

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 5 residues within 4Å: Chain A: V.214, I.215, N.220, A.223 Chain B: D.425 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.214, A:A.223 Hydrogen bonds: A:I.215, A:I.215, B:D.425 NAG.2: 5 residues within 4Å: Chain A: G.54, S.55, S.56, N.89, R.202 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.89, A:R.202 NAG.12: 5 residues within 4Å: Chain B: V.214, I.215, N.220, A.223 Chain C: D.425 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.214, B:A.223 Hydrogen bonds: B:I.215, B:I.215, C:D.425 NAG.13: 5 residues within 4Å: Chain B: G.54, S.55, S.56, N.89, R.202 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.89, B:R.202 NAG.23: 5 residues within 4Å: Chain A: D.425 Chain C: V.214, I.215, N.220, A.223 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:D.425, C:I.215, C:I.215 Hydrophobic interactions: C:V.214, C:A.223 NAG.24: 5 residues within 4Å: Chain C: G.54, S.55, S.56, N.89, R.202 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.89, C:R.202

9 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.188, E.257, H.355 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.188, A:E.257, A:H.355 ZN.4: 2 residues within 4Å: Chain A: H.315, N.320 No protein-ligand interaction detected (PLIP) ZN.5: 2 residues within 4Å: Chain A: D.164, D.167 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.164, A:D.167, A:D.167 ZN.14: 3 residues within 4Å: Chain B: H.188, E.257, H.355 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.188, B:E.257, B:H.355 ZN.15: 2 residues within 4Å: Chain B: H.315, N.320 No protein-ligand interaction detected (PLIP) ZN.16: 2 residues within 4Å: Chain B: D.164, D.167 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.164, B:D.167, B:D.167 ZN.25: 3 residues within 4Å: Chain C: H.188, E.257, H.355 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.188, C:E.257, C:H.355 ZN.26: 2 residues within 4Å: Chain C: H.315, N.320 No protein-ligand interaction detected (PLIP) ZN.27: 2 residues within 4Å: Chain C: D.164, D.167 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.164, C:D.167, C:D.167

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 5 residues within 4Å: Chain A: F.247, F.250, R.342 Chain C: E.248, R.279 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.247, C:E.248 Salt bridges: A:R.342, C:R.279 Water bridges: C:R.279 ACT.17: 5 residues within 4Å: Chain A: E.248, R.279 Chain B: F.247, F.250, R.342 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.247, A:E.248 Salt bridges: B:R.342, A:R.279 Water bridges: A:R.279 ACT.28: 5 residues within 4Å: Chain B: E.248, R.279 Chain C: F.247, F.250, R.342 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.247, B:E.248 Salt bridges: C:R.342, B:R.279 Water bridges: B:R.279

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: S.243, I.244, P.245, I.359, G.360, V.361, T.362 No protein-ligand interaction detected (PLIP) GOL.8: 4 residues within 4Å: Chain A: S.212, T.224, A.225, N.226 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.212, A:S.212, A:T.224, A:N.226 GOL.9: 3 residues within 4Å: Chain A: G.341, F.343, E.344 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.343, A:E.344 GOL.10: 3 residues within 4Å: Chain A: K.108, W.311, W.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.108, A:K.108 GOL.11: 4 residues within 4Å: Chain A: K.388, I.389, D.477, R.478 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.477 GOL.18: 7 residues within 4Å: Chain B: S.243, I.244, P.245, I.359, G.360, V.361, T.362 No protein-ligand interaction detected (PLIP) GOL.19: 4 residues within 4Å: Chain B: S.212, T.224, A.225, N.226 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.212, B:S.212, B:T.224, B:N.226 GOL.20: 3 residues within 4Å: Chain B: G.341, F.343, E.344 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.343, B:E.344 GOL.21: 3 residues within 4Å: Chain B: K.108, W.311, W.319 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.108, B:K.108 GOL.22: 4 residues within 4Å: Chain B: K.388, I.389, D.477, R.478 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.477 GOL.29: 7 residues within 4Å: Chain C: S.243, I.244, P.245, I.359, G.360, V.361, T.362 No protein-ligand interaction detected (PLIP) GOL.30: 4 residues within 4Å: Chain C: S.212, T.224, A.225, N.226 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.212, C:S.212, C:T.224, C:N.226 GOL.31: 3 residues within 4Å: Chain C: G.341, F.343, E.344 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.343, C:E.344 GOL.32: 3 residues within 4Å: Chain C: K.108, W.311, W.319 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.108, C:K.108 GOL.33: 4 residues within 4Å: Chain C: K.388, I.389, D.477, R.478 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.477

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedry, J. et al., Evolutionary diversification of the HAP2 membrane insertion motifs to drive gamete fusion across eukaryotes. PLoS Biol. (2018)

Release Date

2018-08-22

Peptides

Protein HAPLESS 2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

C
C

Protein HAPLESS 2