SMTL ID : 6tsr.1

Marasmius oreades agglutinin (MOA) activated by manganese (II) and calcium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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: 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.44 Hydrogen bonds: A:L.21, A:D.23, A:H.45, A:Q.46, A:T.38, A:T.38, A:N.43 Water bridges: A:D.23, A:D.23, A:D.20, A:W.35, A:N.43, A:W.44, A:D.131 Salt bridges: A:H.45 GAL-FUC-GLA.15: 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.19 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.44 Hydrogen bonds: B:L.21, B:D.23, B:Q.46, B:T.38, B:T.38, B:T.38, B:N.43 Salt bridges: B:H.45 Water bridges: B:D.20, B:W.35, B:T.41, B:N.43, B:W.44, B:D.131

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

GLA-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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.95, A:Q.98 Water bridges: A:W.87, A:Q.88, A:Q.88, 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.139, A:E.144, A:N.146, A:Q.149 Water bridges: A:W.138, A:T.139 GLA-FUC-GLA.16: 9 residues within 4Å: Chain B: D.72, L.73, Y.74, N.75, W.87, Q.88, N.95, H.97, Q.98 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.95, B:Q.98 Water bridges: B:W.87, B:Q.88, B:Q.88, B:T.93, B:Q.98 GLA-FUC-GLA.17: 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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.144, B:N.146, B:Q.149 Water bridges: B:W.138, B:T.139, B:T.139

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

EDO.4: 6 residues within 4Å: Chain A: S.206, Y.213 Chain B: K.228, A.231, D.232 Ligands: EDO.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.228 Water bridges: A:K.207 EDO.5: 5 residues within 4Å: Chain A: D.23, H.45, F.66 Ligands: GAL-FUC-GLA.1, GAL-FUC-GLA.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.23, A:D.23 EDO.6: 7 residues within 4Å: Chain A: S.201, G.202, L.203, S.206, Y.213 Chain B: K.228 Ligands: EDO.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.202, A:Y.213, B:K.228 EDO.7: 8 residues within 4Å: Chain A: D.214, C.215, D.216, L.247, Y.289 Chain B: L.182 Ligands: CA.12, MN.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.289 EDO.18: 6 residues within 4Å: Chain A: K.228, A.231, D.232 Chain B: S.206, Y.213 Ligands: EDO.20 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:K.207, A:D.232, A:D.232 Hydrogen bonds: A:K.228 EDO.19: 5 residues within 4Å: Chain B: D.23, H.45, F.66 Ligands: GAL-FUC-GLA.15, GAL-FUC-GLA.15 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.23, B:D.23 EDO.20: 7 residues within 4Å: Chain A: K.228 Chain B: S.201, G.202, L.203, S.206, Y.213 Ligands: EDO.18 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.202, A:K.228 EDO.21: 8 residues within 4Å: Chain A: L.182 Chain B: D.214, C.215, D.216, L.247, Y.289 Ligands: CA.26, MN.28 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:L.182, A:D.183 Hydrogen bonds: B:Y.289

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

DMS.8: 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.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.22: 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.23: 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:V.56, A:V.56, A:D.58 NA.24: 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, B:D.58

4 x CA: CALCIUM ION(Non-covalent)

CA.11: 7 residues within 4Å: Chain A: Q.211, D.214, D.216, D.217 Chain B: D.183 Ligands: CA.12, MN.14 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: 7 residues within 4Å: Chain A: D.214, D.216 Chain B: L.182, D.183 Ligands: EDO.7, CA.11, MN.14 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:L.182, B:D.183, A:D.214, A:D.216, H2O.7 CA.25: 7 residues within 4Å: Chain A: D.183 Chain B: Q.211, D.214, D.216, D.217 Ligands: CA.26, MN.28 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.26: 7 residues within 4Å: Chain A: L.182, D.183 Chain B: D.214, D.216 Ligands: EDO.21, CA.25, MN.28 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.214, B:D.216, A:L.182, A:D.183, H2O.16

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.13: 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.5, H2O.6 MN.14: 7 residues within 4Å: Chain A: D.214, D.216 Chain B: L.182, D.183 Ligands: EDO.7, CA.11, CA.12 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:L.182, B:D.183, A:D.214, A:D.216, H2O.7 MN.27: 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.12, H2O.13, H2O.14 MN.28: 7 residues within 4Å: Chain A: L.182, D.183 Chain B: D.214, D.216 Ligands: EDO.21, CA.25, CA.26 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.214, B:D.216, A:L.182, A:D.183, H2O.16

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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