SMTL ID : 8vcs.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-octamer

Ligands

11 x GLC- GAL: beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GAL.1: 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.21, A:D.37, A:H.39, A:H.35 Water bridges: A:E.121 GLC-GAL.2: 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, R.89 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.66, B:G.69, B:D.85, B:H.87, B:R.89 Salt bridges: B:H.83 GLC-GAL.3: 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.110, B:P.111, B:G.113, B:G.114, B:D.129, B:D.129, B:H.131, B:H.127 GLC-GAL.4: 9 residues within 4Å: Chain C: E.77, H.110, P.111, K.112, G.113, G.114, V.125, H.127, H.131 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.113, C:G.114, C:H.131, C:H.127 GLC-GAL.5: 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 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.111, D:G.113, D:G.114, D:D.129, D:H.131, D:E.77 Water bridges: D:N.76 GLC-GAL.6: 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, R.89 Chain H: K.142 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain H Hydrogen bonds: E:P.67, E:G.69, E:H.87, E:R.89, E:H.83 Salt bridges: H:K.142 GLC-GAL.7: 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 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:H.110, E:P.111, E:G.113, E:D.129, E:D.129, E:H.131, E:E.77, E:K.112, E:G.113 GLC-GAL.8: 9 residues within 4Å: Chain E: H.18, P.19, K.20, G.21, G.22, H.35, D.37, H.39, E.121 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.21, E:D.37, E:H.39 GLC-GAL.9: 10 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 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:P.111, G:G.113, G:D.129, G:H.131, G:H.127 GLC-GAL.10: 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:P.111, H:G.113, H:D.129, H:H.131 GLC-GAL.11: 9 residues within 4Å: Chain H: H.18, P.19, K.20, G.21, G.22, H.35, D.37, H.39, E.121 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:H.18, H:P.19, H:G.21, H:D.37 Salt bridges: H:H.35

12 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.12: 10 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.110, A:P.111, A:G.113, A:D.129, A:D.129, A:H.131 GAL.13: 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:P.67, A:G.69, A:D.85, A:H.87, A:R.89 Salt bridges: A:H.83 GAL.14: 8 residues within 4Å: Chain B: H.18, P.19, K.20, G.21, G.22, D.37, H.39, E.121 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.18, B:P.19, B:G.21, B:D.37, B:D.37, B:H.39 GAL.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 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.18, C:P.19, C:G.21, C:D.37, C:H.39 GAL.16: 10 residues within 4Å: Chain C: D.29, H.66, P.67, L.68, G.69, G.70, V.81, H.83, D.85, H.87 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.66, C:G.69, C:D.85 GAL.17: 10 residues within 4Å: Chain D: H.18, P.19, K.20, G.21, G.22, H.35, D.37, H.39, R.41, E.121 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:P.19, D:G.21, D:H.39, D:R.41 GAL.18: 6 residues within 4Å: Chain D: D.29, H.66, P.67, G.69, H.83, D.85 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.29, D:G.69, D:D.85 Salt bridges: D:H.66, D:H.83 GAL.19: 10 residues within 4Å: Chain F: H.18, P.19, K.20, G.21, G.22, V.33, H.35, D.37, H.39, E.121 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:H.18, F:P.19, F:G.21, F:D.37, F:H.39 Salt bridges: F:H.35 GAL.20: 10 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 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:H.110, F:P.111, F:G.113, F:D.129, F:H.131 GAL.21: 7 residues within 4Å: Chain F: D.29, P.67, L.68, G.69, V.81, H.83, D.85 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:D.29, F:G.69, F:D.85, F:D.85 Salt bridges: F:H.66, F:H.83 GAL.22: 10 residues within 4Å: Chain G: H.18, P.19, K.20, G.21, G.22, H.35, D.37, H.39, R.41, E.121 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:H.18, G:P.19, G:G.21, G:G.22, G:H.35, G:D.37, G:R.41, G:R.41 GAL.24: 10 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 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:P.67, H:G.69, H:H.87

1 x CA: CALCIUM ION(Non-functional Binders)

CA.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

Related Entries With Identical Sequence