SMTL ID : 8vcq.1

Crystal structure of the oligomeric rMcL-1 in complex with raffinose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-octamer

Ligands

26 x FRU- GLC- GLA: alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose

FRU-GLC-GLA.1: 10 residues within 4Å: Chain D: E.77, H.110, P.111, K.112, G.113, G.114, V.125, H.127, D.129, H.131 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:H.127, D:H.110, D:P.111, D:G.113, D:D.129, D:D.129, D:H.131 Water bridges: D:N.76 FRU-GLC-GLA.2: 10 residues within 4Å: Chain F: D.29, H.66, P.67, L.68, G.69, G.70, V.81, H.83, D.85, H.87 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:P.67, F:G.69, F:H.87, F:H.83 Water bridges: F:R.89, F:R.89 FRU-GLC-GLA.3: 11 residues within 4Å: Chain F: E.77, H.110, P.111, K.112, G.113, G.114, V.125, H.127, D.129, H.131 Ligands: EPE.31 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:H.127, F:P.111, F:G.113, F:D.129, F:D.129, F:H.131 FRU-GLC-GLA.4: 11 residues within 4Å: Chain G: E.77, H.110, P.111, K.112, G.113, G.114, V.125, H.127, D.129, H.131 Ligands: GLA.35 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:D.129, G:H.110, G:P.111, G:G.113, G:D.129, G:D.129, G:H.131 FRU-GLC-GLA.5: 11 residues within 4Å: Chain H: D.29, H.66, P.67, L.68, G.69, G.70, V.81, H.83, D.85, H.87 Ligands: FRU-GLC-GLA.23 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:H.66, H:P.67, H:G.69, H:D.85, H:H.87, H:H.83 Water bridges: H:H.87, H:R.89, H:R.89 FRU-GLC-GLA.6: 10 residues within 4Å: Chain H: E.77, H.110, P.111, K.112, G.113, G.114, V.125, H.127, D.129, H.131 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:H.127, H:H.110, H:P.111, H:G.113, H:H.131 FRU-GLC-GLA.7: 12 residues within 4Å: Chain E: D.29, H.66, P.67, L.68, G.69, G.70, V.81, H.83, D.85, H.87 Chain H: K.142, K.146 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain H Hydrogen bonds: E:H.66, E:P.67, E:G.69, E:D.85, E:H.87, H:K.146, E:H.83 FRU-GLC-GLA.8: 10 residues within 4Å: Chain E: E.77, H.110, P.111, K.112, G.113, G.114, V.125, H.127, D.129, H.131 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.129, E:E.77, E:G.113, E:D.129, E:H.131 FRU-GLC-GLA.9: 11 residues within 4Å: Chain A: E.77, H.110, P.111, K.112, G.113, G.114, V.125, H.127, D.129, H.131 Ligands: GLA.27 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.127, A:P.111, A:G.113, A:G.114, A:D.129, A:H.131 FRU-GLC-GLA.10: 10 residues within 4Å: Chain B: E.77, H.110, P.111, K.112, G.113, G.114, V.125, H.127, D.129, H.131 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.127, B:P.111, B:G.113, B:H.131 FRU-GLC-GLA.11: 10 residues within 4Å: Chain A: H.18, P.19, K.20, G.21, G.22, V.33, H.35, D.37, H.39, E.121 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.121, A:H.18, A:G.21, A:D.37, A:H.39 FRU-GLC-GLA.12: 10 residues within 4Å: Chain A: D.29, H.66, P.67, L.68, G.69, G.70, H.83, D.85, H.87, R.89 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.66, A:P.67, A:G.69, A:D.85, A:H.87, A:R.89 FRU-GLC-GLA.13: 10 residues within 4Å: Chain B: H.18, P.19, K.20, G.21, G.22, V.33, H.35, D.37, H.39, E.121 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.35, B:P.19, B:G.21, B:H.39 FRU-GLC-GLA.14: 11 residues within 4Å: Chain B: D.29, H.66, P.67, L.68, G.69, G.70, V.81, H.83, D.85, H.87 Ligands: FRU-GLC-GLA.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.67, B:G.69, B:H.87, B:H.83 Water bridges: B:R.89, B:R.89, B:R.89, B:N.28 FRU-GLC-GLA.15: 10 residues within 4Å: Chain C: H.18, P.19, K.20, G.21, G.22, V.33, H.35, D.37, H.39, E.121 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.20, C:K.20, C:G.21, C:H.39, C:H.35, C:E.121 Water bridges: C:R.41, C:R.41 FRU-GLC-GLA.16: 9 residues within 4Å: Chain C: E.77, H.110, P.111, K.112, G.113, G.114, H.127, D.129, H.131 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.110, C:G.113, C:D.129, C:D.129, C:H.131, C:E.77, C:H.127 FRU-GLC-GLA.17: 10 residues within 4Å: Chain E: H.18, P.19, K.20, G.21, G.22, V.33, H.35, D.37, H.39, E.121 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.18, E:P.19, E:G.21, E:D.37, E:H.39, E:E.121, E:H.35 Water bridges: E:R.41, E:R.41 FRU-GLC-GLA.18: 10 residues within 4Å: Chain G: H.18, P.19, K.20, G.21, G.22, V.33, H.35, D.37, H.39, E.121 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.21, G:P.19, G:G.21, G:H.39, G:H.35 FRU-GLC-GLA.19: 10 residues within 4Å: Chain G: D.29, H.66, P.67, L.68, G.69, G.70, V.81, H.83, D.85, H.87 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:P.67, G:G.69, G:G.70, G:H.87, G:R.89, G:H.83 FRU-GLC-GLA.20: 10 residues within 4Å: Chain H: H.18, P.19, K.20, G.21, G.22, V.33, H.35, D.37, H.39, E.121 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:H.18, H:G.21, H:D.37, H:H.39, H:H.35 FRU-GLC-GLA.21: 12 residues within 4Å: Chain D: H.18, P.19, K.20, G.21, G.22, V.33, H.35, D.37, H.39, E.121 Chain H: K.11, A.12 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain D Hydrogen bonds: H:A.12, D:H.18, D:P.19, D:G.21, D:G.22, D:D.37, D:H.39, D:H.35 Water bridges: D:N.120 FRU-GLC-GLA.22: 12 residues within 4Å: Chain B: K.11, A.12 Chain F: H.18, P.19, K.20, G.21, G.22, V.33, H.35, D.37, H.39, E.121 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:P.19, F:G.21, F:G.22, F:H.39, F:H.35, F:E.121 FRU-GLC-GLA.23: 4 residues within 4Å: Chain H: H.83, Q.84, D.85 Ligands: FRU-GLC-GLA.5 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Q.84 FRU-GLC-GLA.24: 4 residues within 4Å: Chain B: H.83, Q.84, D.85 Ligands: FRU-GLC-GLA.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.84 Water bridges: B:N.28 FRU-GLC-GLA.25: 10 residues within 4Å: Chain B: K.146 Chain C: D.29, H.66, P.67, L.68, G.69, G.70, H.83, D.85, H.87 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:P.67, C:G.69, C:H.87, C:H.83, B:K.146 FRU-GLC-GLA.26: 10 residues within 4Å: Chain D: D.29, H.66, P.67, L.68, G.69, G.70, V.81, H.83, D.85, H.87 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.29, D:D.29, D:H.66, D:P.67, D:G.69, D:D.85, D:H.87, D:H.83 Water bridges: D:R.89, D:R.89

2 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.27: 4 residues within 4Å: Chain A: G.114, D.129, H.131 Ligands: FRU-GLC-GLA.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.131 GLA.35: 5 residues within 4Å: Chain G: G.114, D.129, H.131 Ligands: FRU-GLC-GLA.4, FRU-GLC-GLA.4 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:D.129, G:D.129, G:H.131 Salt bridges: G:H.131

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.28: 5 residues within 4Å: Chain D: G.113, G.114, H.131, K.132, A.133 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.132 EPE.31: 7 residues within 4Å: Chain F: G.113, G.114, S.115, T.116, H.131, K.132 Ligands: FRU-GLC-GLA.3 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:H.131, F:K.132 Water bridges: F:T.116

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

PG4.29: 2 residues within 4Å: Chain D: Q.84, D.85 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.84 PG4.33: 2 residues within 4Å: Chain F: Q.84, D.85 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.84, F:D.85

1 x CA: CALCIUM ION(Non-covalent)

CA.30: 1 residues within 4Å: Chain D: N.28 No protein-ligand interaction detected (PLIP)

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

ACT.32: 3 residues within 4Å: Chain F: H.87, D.88, R.89 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:H.87 Hydrogen bonds: F:D.88 Salt bridges: F:R.89

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.34: 2 residues within 4Å: Chain F: A.27, N.28 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.28, F:N.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loera-Rubalcava, J. et al., A mytilectin from Mytilus californianus: Study of its unique galactoside interactions, oligomerization patterns, and antifungal activity. Int.J.Biol.Macromol. (2025)

Release Date

2024-12-18

Peptides

Galactose-binding lectin: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Galactose-binding lectin

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