SMTL ID : 6tso.1

Marasmius oreades agglutinin (MOA) inhibited by cadmium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x GAL- FUC- GLA: alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose

GAL-FUC-GLA.1: 12 residues within 4Å: Chain A: D.20, L.21, K.22, D.23, W.35, Q.36, F.37, T.38, N.43, W.44, H.45, Q.46 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.44 Hydrogen bonds: A:L.21, A:D.23, A:H.45, A:T.38, A:T.38, A:N.43, A:Q.46 Water bridges: A:D.23, A:D.23, A:H.45, A:W.44 Salt bridges: A:H.45 GAL-FUC-GLA.10: 12 residues within 4Å: Chain B: D.20, L.21, K.22, D.23, W.35, Q.36, F.37, T.38, N.43, W.44, H.45, Q.46 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.44 Hydrogen bonds: B:L.21, B:D.23, B:T.38, B:T.38, B:T.38, B:N.43, B:Q.46 Water bridges: B:H.45, B:T.41, B:W.44 Salt bridges: B:H.45

4 x GLA- FUC- GLA: alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose

GLA-FUC-GLA.2: 8 residues within 4Å: Chain A: D.72, L.73, Y.74, N.75, W.87, Q.88, N.95, H.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.95, A:Q.98, A:Q.98 GLA-FUC-GLA.3: 11 residues within 4Å: Chain A: D.123, L.124, V.125, N.126, W.138, T.139, G.140, E.144, N.146, H.148, Q.149 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.139, A:E.144, A:N.146, A:Q.149 Water bridges: A:W.138 GLA-FUC-GLA.11: 8 residues within 4Å: Chain B: D.72, L.73, Y.74, N.75, W.87, Q.88, N.95, H.97 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.95, B:Q.98, B:Q.98 GLA-FUC-GLA.12: 11 residues within 4Å: Chain B: D.123, L.124, V.125, N.126, W.138, T.139, G.140, E.144, N.146, H.148, Q.149 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.144, B:N.146, B:Q.149 Water bridges: B:W.138

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: D.214, C.215, D.216, L.247, A.256 Chain B: L.182 Ligands: CA.6 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.183 EDO.13: 7 residues within 4Å: Chain A: L.182 Chain B: D.214, C.215, D.216, L.247, A.256 Ligands: CA.15 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: Q.211, D.214, D.216, D.217 Chain B: D.183 Ligands: CA.6 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Metal complexes: A:Q.211, A:D.214, A:D.216, A:D.217, B:D.183 CA.6: 6 residues within 4Å: Chain A: D.214, D.216 Chain B: L.182, D.183 Ligands: EDO.4, CA.5 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.214, A:D.216, B:L.182, B:D.183, H2O.8 CA.14: 6 residues within 4Å: Chain A: D.183 Chain B: Q.211, D.214, D.216, D.217 Ligands: CA.15 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Metal complexes: B:Q.211, B:D.214, B:D.216, B:D.217, A:D.183 CA.15: 6 residues within 4Å: Chain A: L.182, D.183 Chain B: D.214, D.216 Ligands: EDO.13, CA.14 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:L.182, A:D.183, B:D.214, B:D.216, H2O.4

2 x NA: SODIUM ION(Non-functional Binders)

NA.7: 2 residues within 4Å: Chain A: I.53, V.56 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.56, A:V.56 Water bridges: A:D.58 NA.16: 2 residues within 4Å: Chain B: I.53, V.56 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.53, B:V.56 Water bridges: B:D.58

4 x CD: CADMIUM ION(Non-covalent)

CD.8: 2 residues within 4Å: Chain A: C.215, H.257 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.215, A:H.257, H2O.2 CD.9: 2 residues within 4Å: Chain A: H.172, D.287 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.172, A:D.287, H2O.3, H2O.3, H2O.4 CD.17: 2 residues within 4Å: Chain B: C.215, H.257 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.215, B:H.257, H2O.5 CD.18: 2 residues within 4Å: Chain B: H.172, D.287 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.172, B:D.287, H2O.7, H2O.7, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manna, D. et al., Crystal structure of MOA in complex with a peptide fragment: A protease caught in flagranti . Curr Res Struct Biol (2020)

Release Date

2020-07-29

Peptides

Agglutinin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

Agglutinin

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