SMTL ID : 8vcp.1

Crystal structure of dimeric rMcL-1 in complex with raffinose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

6 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 A: 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 A Hydrogen bonds: A:P.67, A:G.69, A:H.87, A:D.29 Water bridges: A:G.69, A:R.89, A:R.89, A:R.89, A:R.89, A:N.28, A:H.83 FRU-GLC-GLA.2: 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:H.18, A:P.19, A:G.21, A:D.37, A:H.39, A:H.35 Water bridges: A:R.41, A:R.41, A:N.120 FRU-GLC-GLA.3: 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.110, A:P.111, A:G.113, A:D.129, A:D.129, A:H.131, A:E.77 FRU-GLC-GLA.4: 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 Water bridges: B:G.113 Hydrogen bonds: B:P.111, B:G.113, B:G.114, B:H.131, B:H.127 FRU-GLC-GLA.5: 11 residues within 4Å: Chain B: N.28, D.29, H.66, P.67, L.68, G.69, G.70, V.81, H.83, D.85, H.87 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:G.69, B:R.89, B:N.28 FRU-GLC-GLA.6: 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.19, B:G.21, B:H.39 Water bridges: B:H.39

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 3 residues within 4Å: Chain A: V.148, L.149 Chain B: E.51 No protein-ligand interaction detected (PLIP)

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

ACT.8: 2 residues within 4Å: Chain B: S.115, T.116 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.116

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: R.147 Chain B: R.52, W.53 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.53, A:R.147 Water bridges: A:K.146

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Galactose-binding lectin

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