SMTL ID : 5mr3.1 (1 other biounit)

Crystal structure of red abalone egg VERL repeat 2 with linker in complex with sperm lysin at 1.8 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-mer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: W.68, K.72, E.91, R.95 Chain B: L.64, L.65 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.68, A:K.72, A:E.91, A:R.95 GOL.2: 9 residues within 4Å: Chain A: M.110 Chain B: D.5, W.6, D.7, F.9, I.21, S.22, R.23 Chain D: K.81 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.5, B:I.21, B:R.23 GOL.3: 6 residues within 4Å: Chain B: V.79, P.80, N.82, V.85, Y.109 Ligands: NAG.6 No protein-ligand interaction detected (PLIP) GOL.5: 9 residues within 4Å: Chain B: R.93, D.103 Chain D: S.40, F.73, W.74, G.75, P.76, Y.77 Ligands: GOL.9 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:G.75, D:P.76, D:Y.77, D:Y.77, B:R.93 Water bridges: B:R.93 GOL.7: 7 residues within 4Å: Chain C: K.48, Y.51, R.55, Y.114, E.119, N.122, R.123 No protein-ligand interaction detected (PLIP) GOL.8: 8 residues within 4Å: Chain B: P.76, Y.77, S.78, V.86, K.112 Chain D: P.101, T.102, D.103 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:S.78, D:D.103, D:D.103, D:D.103, D:D.103 GOL.9: 8 residues within 4Å: Chain B: D.38, T.91 Chain D: D.38, W.74, Y.77, T.89, T.91 Ligands: GOL.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Water bridges: B:D.38, B:D.38, B:T.91, D:Y.77 GOL.10: 10 residues within 4Å: Chain B: E.120 Chain D: T.2, G.3, L.30, W.96, E.98, G.99, P.100, P.101, T.102 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:E.120, D:P.100, D:T.102, D:T.102

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

CL.4: 3 residues within 4Å: Chain B: W.74, G.75, Y.77 Ligand excluded by PLIP

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

NAG.6: 7 residues within 4Å: Chain B: K.81, N.82, T.84, V.85, P.111, K.112 Ligands: GOL.3 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.85, B:P.111 Hydrogen bonds: B:N.82 NAG.11: 5 residues within 4Å: Chain D: K.81, N.82, T.84, V.85, Y.109 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raj, I. et al., Structural Basis of Egg Coat-Sperm Recognition at Fertilization. Cell (2017)

Release Date

2017-06-14

Peptides

Egg-lysin: AC
Vitelline envelope sperm lysin receptor: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Egg-lysin

Vitelline envelope sperm lysin receptor

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