SMTL ID : 8vco.1

Crystal structure of rMcL-1 in complex with N-acetyl-D-galactosamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

5 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.1: 11 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, R.89 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.67, A:G.69, A:H.87, A:R.89 Salt bridges: A:H.83 A2G.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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.18, A:P.19, A:G.21, A:H.39 Water bridges: A:E.121, A:E.121, A:E.121 Salt bridges: A:H.35 A2G.7: 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.111, B:G.113, B:H.131 Salt bridges: B:H.127 A2G.8: 12 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 Ligands: GOL.13 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:H.66, B:P.67, B:G.69, B:D.85, B:D.85, B:H.87, B:R.89 Water bridges: B:D.85 Salt bridges: B:H.83 A2G.9: 11 residues within 4Å: Chain B: H.18, P.19, K.20, G.21, G.22, V.33, H.35, D.37, H.39, R.41, E.121 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.19, B:G.21, B:D.37, B:H.39, B:R.41 Salt bridges: B:H.35

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: N.76, E.77, H.127 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.127 Water bridges: A:N.76, A:N.76 GOL.4: 3 residues within 4Å: Chain A: R.52, W.53 Chain B: R.147 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:W.53, B:R.147 Water bridges: B:R.147, B:R.147, B:R.147 GOL.5: 2 residues within 4Å: Chain A: D.129 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.129 Water bridges: A:D.129 GOL.10: 3 residues within 4Å: Chain A: R.147 Chain B: R.52, W.53 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.147 Water bridges: A:R.147, B:R.52 GOL.11: 4 residues within 4Å: Chain B: D.73, P.74, P.75, K.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.74, B:K.107 GOL.12: 5 residues within 4Å: Chain B: K.20, S.23, P.26, A.27, T.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.27, B:T.30, B:T.30 GOL.13: 4 residues within 4Å: Chain B: N.28, D.29, H.83 Ligands: A2G.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.29 Water bridges: B:D.85

1 x 01: N-Acetyl-D-Talosamine

01.6: 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 8 PLIP interactions: 8 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:H.131 Salt bridges: A:H.127

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

ACT.14: 4 residues within 4Å: Chain B: D.50, D.88, L.91, K.104 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.50 Salt bridges: B:K.104

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.15: 3 residues within 4Å: Chain B: Q.84, D.85, R.86 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.84, B:D.85 Water bridges: B:G.62, B:R.86

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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