SMTL ID : 8vcu.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-tetramer

Ligands

16 x FRU- GAL: beta-D-galactopyranose-(1-4)-beta-D-fructofuranose(Non-covalent)

FRU-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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.19, A:G.21, A:D.37, A:H.39 Water bridges: A:R.41, A:R.41 FRU-GAL.2: 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 6 PLIP interactions: 6 interactions with chain A Water bridges: A:G.69, A:G.69, A:D.85 Hydrogen bonds: A:H.66, A:P.67, A:G.69, A:D.85, A:H.87 FRU-GAL.3: 12 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 Chain D: S.115, T.116 12 PLIP interactions: 5 interactions with chain D, 7 interactions with chain A Hydrogen bonds: D:T.116, D:T.116, A:H.110, A:P.111, A:G.113, A:D.129, A:D.129, A:H.131 Water bridges: D:S.115, D:S.115, D:T.116, A:G.113 FRU-GAL.4: 6 residues within 4Å: Chain A: R.52, W.53, K.104, A.105, G.106 Chain B: R.147 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.104, A:K.104, B:R.147, B:R.147 Water bridges: A:R.52, A:W.53, B:K.11, B:K.11 FRU-GAL.5: 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:D.37, B:H.39 FRU-GAL.6: 10 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 5 PLIP interactions: 5 interactions with chain B Water bridges: B:G.69, B:H.83 Hydrogen bonds: B:H.66, B:P.67, B:G.69, B:D.85, B:H.87 FRU-GAL.7: 13 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 Chain C: G.114, S.115, T.116 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:T.116, C:T.116, B:H.110, B:P.111, B:G.113, B:D.129, B:D.129, B:H.131 Water bridges: C:T.116 FRU-GAL.8: 8 residues within 4Å: Chain A: D.99, R.147 Chain B: R.52, W.53, K.104, A.105, G.106 Ligands: GOL.17 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Water bridges: B:K.104, B:R.52, B:R.52, B:W.53, B:W.53, A:R.147 Hydrogen bonds: A:D.99, A:R.147 FRU-GAL.9: 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 8 PLIP interactions: 8 interactions with chain C Water bridges: C:G.21, C:R.41, C:R.41 Hydrogen bonds: C:H.18, C:P.19, C:G.21, C:D.37, C:D.37, C:H.39 FRU-GAL.10: 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 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:P.67, C:G.69, C:H.87 Water bridges: C:G.69, C:D.85, C:R.89, C:R.89 FRU-GAL.11: 12 residues within 4Å: Chain B: S.115, T.116 Chain C: E.77, H.110, P.111, K.112, G.113, G.114, V.125, H.127, D.129, H.131 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Water bridges: C:G.113, B:S.115, B:S.115, B:S.115, B:G.114 Hydrogen bonds: B:T.116, B:T.116, C:P.111, C:G.113, C:G.114, C:D.129, C:H.131 FRU-GAL.12: 6 residues within 4Å: Chain C: R.52, W.53, K.104, G.106 Chain D: D.99, R.147 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Water bridges: C:A.105, C:R.52, C:R.52, C:R.52, C:W.53, C:W.53, C:K.104 Hydrogen bonds: D:D.99, D:R.147, D:R.147 FRU-GAL.13: 10 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 11 PLIP interactions: 11 interactions with chain D Water bridges: D:K.20, D:K.20, D:G.21, D:R.41, D:R.41, D:R.41 Hydrogen bonds: D:H.18, D:P.19, D:G.21, D:D.37, D:D.37, D:H.39 FRU-GAL.14: 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 5 PLIP interactions: 5 interactions with chain D Water bridges: D:G.69, D:G.69, D:G.69, D:R.89 Hydrogen bonds: D:P.67, D:G.69, D:H.87 FRU-GAL.15: 12 residues within 4Å: Chain A: S.115, T.116 Chain D: E.77, H.110, P.111, K.112, G.113, G.114, V.125, H.127, D.129, H.131 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:T.116, A:T.116, D:P.111, D:G.113, D:D.129, D:H.131 Water bridges: A:S.115, A:S.115, D:G.113 FRU-GAL.16: 6 residues within 4Å: Chain C: R.147 Chain D: R.52, W.53, K.104, A.105, G.106 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:K.104, C:R.147, C:R.147 Water bridges: D:R.52, D:R.52, D:W.53, C:K.11, C:K.11, C:K.11, C:D.99

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 3 residues within 4Å: Chain A: K.11, R.147 Ligands: FRU-GAL.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.11, A:K.11, A:R.147 Water bridges: A:D.145, A:R.147

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

ACT.18: 5 residues within 4Å: Chain A: K.9, S.13, G.14, K.144, D.145 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.9 Salt bridges: A:K.9, A:K.144 ACT.19: 5 residues within 4Å: Chain B: K.9, K.11, G.14, K.144, D.145 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.9, B:D.145 Salt bridges: B:K.9, B:K.144 ACT.21: 4 residues within 4Å: Chain D: K.9, G.14, K.144, D.145 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.9, D:K.144

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

PEG.20: 7 residues within 4Å: Chain C: K.9, K.11, S.13, G.14, F.16, K.144, D.145 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.11, C:G.14, C:K.144

1 x NI: NICKEL (II) ION(Non-covalent)

NI.22: 1 residues within 4Å: Chain D: R.52 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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Galactose-binding lectin

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