SMTL ID : 6zu2.1

CML1 crystal structure in complex with H-type 1 trisaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-hexamer

Ligands

6 x NAG- GAL- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-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, T.56, W.93 Chain B: R.113 Ligands: SO4.9 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.53, A:N.54, B:R.113, B:R.113, B:R.113 Water bridges: A:N.54, A:Y.55, A:N.54, A:T.56, A:W.93 NAG-GAL-FUC.2: 9 residues within 4Å: Chain A: R.113 Chain B: L.27, H.53, N.54, Y.55, T.56, W.93 Ligands: SO4.7, SO4.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.53, B:N.54, A:R.113, A:R.113, A:R.113 Water bridges: B:N.54, B:Y.55, B:N.28, B:N.54 NAG-GAL-FUC.3: 9 residues within 4Å: Chain C: L.27, H.53, N.54, Y.55, T.56, W.93 Chain D: V.111, R.113 Ligands: SO4.18 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:H.53, C:N.54, D:R.113, D:R.113, D:R.113 Water bridges: C:N.54, C:Y.55, C:N.54 NAG-GAL-FUC.4: 10 residues within 4Å: Chain C: V.111, R.113 Chain D: L.27, H.53, N.54, Y.55, T.56, W.93 Ligands: SO4.14, SO4.15 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:R.113, C:R.113, D:H.53, D:N.54, C:R.113 Hydrophobic interactions: D:L.27 Water bridges: D:N.54, D:Y.55, D:N.28, D:N.28, D:N.28, D:N.54 NAG-GAL-FUC.5: 9 residues within 4Å: Chain E: L.27, H.53, N.54, Y.55, T.56, W.93 Chain F: R.113 Ligands: SO4.20, SO4.23 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, F:R.113 Hydrophobic interactions: E:L.27 Water bridges: E:N.54, E:Y.55, E:N.54 NAG-GAL-FUC.6: 8 residues within 4Å: Chain E: R.113 Chain F: L.27, H.53, N.54, Y.55, T.56, W.93 Ligands: SO4.22 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:H.53, F:N.54, E:R.113, E:R.113, E:R.113 Water bridges: F:N.54, F:Y.55, F:N.54

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

SO4.7: 3 residues within 4Å: Chain A: R.113 Ligands: NAG-GAL-FUC.2, NAG-GAL-FUC.2 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: S.95, S.96, T.97 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain B: R.113 Ligands: NAG-GAL-FUC.1, NAG-GAL-FUC.1 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain B: R.31, V.111 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain B: R.57 Ligands: NAG-GAL-FUC.2 Ligand excluded by PLIP SO4.12: 1 residues within 4Å: Chain C: R.31 Ligand excluded by PLIP SO4.13: 1 residues within 4Å: Chain C: G.109 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain C: R.113 Ligands: NAG-GAL-FUC.4, NAG-GAL-FUC.4 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain D: R.57 Ligands: NAG-GAL-FUC.4 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain D: E.101, D.102 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain D: R.31 Ligands: SO4.18 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain D: V.111, R.113 Ligands: NAG-GAL-FUC.3, SO4.17 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain E: K.18, K.115 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain E: R.57 Ligands: NAG-GAL-FUC.5 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain E: R.31, V.111 Ligands: SO4.22 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain E: R.113 Ligands: NAG-GAL-FUC.6, NAG-GAL-FUC.6, SO4.21 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain F: R.113 Ligands: NAG-GAL-FUC.5, NAG-GAL-FUC.5 Ligand excluded by PLIP

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

2021-07-28

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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