SMTL ID : 6tsp.1

Marasmius oreades agglutinin (MOA) inhibited by zinc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

GAL-FUC-GLA.1: 13 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 Ligands: EDO.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.44 Hydrogen bonds: A:L.21, A:D.23, A:D.23, A:H.45, A:T.38, A:T.38, A:N.43 Water bridges: A:W.44, A:H.45, A:D.20, A:N.43, A:W.44 Salt bridges: A:H.45 GAL-FUC-GLA.2: 9 residues within 4Å: Chain A: D.72, L.73, Y.74, N.75, W.87, Q.88, N.95, H.97, Q.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.73, A:N.75, A:N.95, A:N.95, A:N.95, A:Q.98, A:Q.98 Water bridges: A:D.72, A:N.75 Salt bridges: A:H.97 GAL-FUC-GLA.19: 13 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 Ligands: EDO.23 8 PLIP interactions: 8 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 Water bridges: B:W.44, B:H.45, B:D.20, B:T.41, B:N.43, B:W.44 Salt bridges: B:H.45 GAL-FUC-GLA.20: 9 residues within 4Å: Chain B: D.72, L.73, Y.74, N.75, W.87, Q.88, N.95, H.97, Q.98 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.73, B:N.75, B:N.95, B:N.95, B:H.97, B:N.95, B:Q.98, B:Q.98 Water bridges: B:N.75, B:T.93 Salt bridges: B:H.97

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

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.21: 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

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

EDO.4: 5 residues within 4Å: Chain A: K.228, A.231, D.232 Chain B: S.206, Y.213 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.228 Water bridges: B:K.207 EDO.5: 1 residues within 4Å: Ligands: GAL-FUC-GLA.1 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain A: D.214, C.215, D.216, L.247 Chain B: L.182 Ligands: CA.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.216 EDO.22: 5 residues within 4Å: Chain A: S.206, Y.213 Chain B: K.228, A.231, D.232 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.228 Water bridges: A:K.207 EDO.23: 1 residues within 4Å: Ligands: GAL-FUC-GLA.19 No protein-ligand interaction detected (PLIP) EDO.24: 6 residues within 4Å: Chain A: L.182 Chain B: D.214, C.215, D.216, L.247 Ligands: CA.30 No protein-ligand interaction detected (PLIP)

6 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 6 residues within 4Å: Chain A: A.231, D.232, S.233, W.234, K.235 Chain B: R.209 No protein-ligand interaction detected (PLIP) DMS.8: 3 residues within 4Å: Chain A: S.106, D.107, G.108 No protein-ligand interaction detected (PLIP) DMS.9: 4 residues within 4Å: Chain A: G.24, S.25, S.26, F.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.26 DMS.25: 6 residues within 4Å: Chain A: R.209 Chain B: A.231, D.232, S.233, W.234, K.235 No protein-ligand interaction detected (PLIP) DMS.26: 3 residues within 4Å: Chain B: S.106, D.107, G.108 No protein-ligand interaction detected (PLIP) DMS.27: 4 residues within 4Å: Chain B: G.24, S.25, S.26, F.66 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.26

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

NA.10: 2 residues within 4Å: Chain A: I.53, V.56 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.53, A:V.56, A:D.58 NA.28: 2 residues within 4Å: Chain B: I.53, V.56 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.56, B:V.56, B:D.58

4 x CA: CALCIUM ION(Non-covalent)

CA.11: 6 residues within 4Å: Chain A: Q.211, D.214, D.216, D.217 Chain B: D.183 Ligands: CA.12 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.12: 6 residues within 4Å: Chain A: D.214, D.216 Chain B: L.182, D.183 Ligands: EDO.6, CA.11 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:D.214, A:D.216, B:L.182, B:D.183 CA.29: 6 residues within 4Å: Chain A: D.183 Chain B: Q.211, D.214, D.216, D.217 Ligands: CA.30 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.30: 6 residues within 4Å: Chain A: L.182, D.183 Chain B: D.214, D.216 Ligands: EDO.24, CA.29 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:L.182, A:D.183, B:D.214, B:D.216

12 x ZN: ZINC ION(Non-covalent)

ZN.13: 3 residues within 4Å: Chain A: H.9, E.11, N.154 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.9, A:E.11, H2O.5 ZN.14: 2 residues within 4Å: Chain A: C.215, H.257 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.215, A:H.257, H2O.4, H2O.5 ZN.15: 2 residues within 4Å: Chain A: N.75, H.97 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.97 ZN.16: 1 residues within 4Å: Chain A: H.148 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.148, H2O.6, H2O.6 ZN.17: 2 residues within 4Å: Chain A: H.172, D.287 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.172, A:D.287, H2O.5 ZN.18: 1 residues within 4Å: Chain A: D.283 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.283, A:D.283, H2O.5 ZN.31: 3 residues within 4Å: Chain B: H.9, E.11, N.154 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.9, B:E.11, H2O.10 ZN.32: 2 residues within 4Å: Chain B: C.215, H.257 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.215, B:H.257, H2O.9, H2O.10 ZN.33: 2 residues within 4Å: Chain B: N.75, H.97 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.97 ZN.34: 1 residues within 4Å: Chain B: H.148 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.148, H2O.11, H2O.11 ZN.35: 2 residues within 4Å: Chain B: H.172, D.287 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.172, B:D.287, H2O.10 ZN.36: 1 residues within 4Å: Chain B: D.283 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.283, B:D.283, H2O.11

Links

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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

2020-08-05

Peptides

Agglutinin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

Agglutinin

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