SMTL ID : 6zv5.1

CML1 crystal structure in complex with Lewis a tetrasaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-hexamer

Ligands

4 x NAG- GAL- FUC: beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-FUC.1: 8 residues within 4Å: Chain A: L.27, H.53, N.54, Y.55, W.93 Chain B: R.31, V.111, R.113 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.113, B:R.113, A:H.53, A:N.54, A:W.93, B:R.113 Hydrophobic interactions: A:L.27 Water bridges: A:N.54, A:Y.55, B:R.31, A:N.54 NAG-GAL-FUC.2: 6 residues within 4Å: Chain A: R.113 Chain B: L.27, H.53, N.54, Y.55, W.93 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.53, B:N.54, A:R.113, A:R.113, B:W.93, A:R.113 Water bridges: B:N.54, B:Y.55, A:R.113, B:N.54, A:R.31 NAG-GAL-FUC.5: 7 residues within 4Å: Chain E: L.27, H.53, N.54, Y.55, W.93 Chain F: R.113 Ligands: SO4.13 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:R.113, F:R.113, E:H.53, E:N.54, E:W.93, F:R.113, E:N.54 Water bridges: E:Y.55 NAG-GAL-FUC.6: 10 residues within 4Å: Chain E: R.31, V.33, V.111, R.113 Chain F: L.27, H.53, N.54, Y.55, W.93 Ligands: SO4.12 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:R.113, E:R.113, F:H.53, F:N.54, F:N.54, F:W.93, E:R.113

2 x GLA- NAG- GAL- FUC: beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-galactopyranose

GLA-NAG-GAL-FUC.3: 9 residues within 4Å: Chain C: L.27, H.53, N.54, Y.55, W.93 Chain D: R.31, V.111, R.113 Ligands: SO4.9 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:H.53, C:N.54, D:R.113, D:R.113, C:W.93, D:R.113 Water bridges: C:N.54, C:Y.55, C:N.54, D:R.31, D:R.31 GLA-NAG-GAL-FUC.4: 8 residues within 4Å: Chain C: V.111, R.113 Chain D: L.27, N.28, H.53, N.54, Y.55, W.93 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:H.53, D:N.54, C:R.113, C:R.113, D:W.93, D:N.28, D:N.54, C:R.113 Water bridges: D:N.54, D:Y.55, C:R.113, D:N.28

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 1 residues within 4Å: Chain B: R.57 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.57 Salt bridges: B:R.57 SO4.8: 1 residues within 4Å: Chain C: R.31 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.31 Salt bridges: C:R.31 SO4.9: 3 residues within 4Å: Chain D: R.113 Ligands: GLA-NAG-GAL-FUC.3, GLA-NAG-GAL-FUC.3 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.113 SO4.10: 1 residues within 4Å: Chain D: R.31 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.31, D:N.112 Salt bridges: D:R.31 SO4.11: 1 residues within 4Å: Chain D: R.57 3 PLIP interactions: 3 interactions with chain D Water bridges: D:T.56, D:T.56 Salt bridges: D:R.57 SO4.12: 3 residues within 4Å: Chain E: R.113 Ligands: NAG-GAL-FUC.6, NAG-GAL-FUC.6 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.113 SO4.13: 3 residues within 4Å: Chain F: R.113 Ligands: NAG-GAL-FUC.5, NAG-GAL-FUC.5 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.113 SO4.14: 1 residues within 4Å: Chain F: R.31 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.31 SO4.15: 1 residues within 4Å: Chain F: R.57 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.57 SO4.16: 3 residues within 4Å: Chain F: N.41, T.42, G.43 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:T.42, F:T.42, F:G.43 Water bridges: F:V.44, F:V.44 SO4.17: 3 residues within 4Å: Chain F: S.95, S.96, T.97 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.96, F:T.97 Water bridges: F:S.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bleuler-Martinez, S. et al., Structure-function relationship of a novel fucoside-binding fruiting body lectin from Coprinopsis cinerea exhibiting nematotoxic activity. Glycobiology (2022)

Release Date

2021-08-04

Peptides

Mucin-binding lectin 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

E
EEE

F
FFF

Mucin-binding lectin 1

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