SMTL ID : 5d61.1

MOA-Z-VAD-fmk complex, direct orientation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x PHQ- VAL- ALA- ASP- CF0: Z-VAD-fmk(Non-covalent)

PHQ-VAL-ALA-ASP-CF0.1: 13 residues within 4Å: Chain A: W.208, D.214, C.215, D.216, V.249, G.253, A.256, H.257, A.258, Y.289 Chain B: I.181, L.182 Ligands: CA.10 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.249 Hydrogen bonds: A:W.208, A:C.215, A:D.216, A:A.256, A:A.256, B:L.182 Water bridges: A:A.256, A:A.256, A:Q.276, B:D.183 PHQ-VAL-ALA-ASP-CF0.13: 13 residues within 4Å: Chain A: I.181, L.182 Chain B: W.208, D.214, C.215, D.216, V.249, G.253, A.256, H.257, A.258, Y.289 Ligands: CA.22 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.249 Hydrogen bonds: B:D.214, B:C.215, B:A.256, A:L.182 Water bridges: B:W.208, B:A.256, B:A.256, B:Q.276

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

GAL-FUC-GLA.2: 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 7 PLIP interactions: 7 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 Salt bridges: A:H.45 Water bridges: A:D.20, A:W.35, A:N.43, A:W.44 GAL-FUC-GLA.14: 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 9 PLIP interactions: 9 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 Salt bridges: B:H.45 Water bridges: B:D.20, B:W.35, B:T.41, B:N.43, B:W.44

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

GLA-FUC-GLA.3: 10 residues within 4Å: Chain A: D.72, L.73, Y.74, N.75, W.87, Q.88, N.95, H.97, Q.98 Ligands: DMS.11 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.4: 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.15: 10 residues within 4Å: Chain B: D.72, L.73, Y.74, N.75, W.87, Q.88, N.95, H.97, Q.98 Ligands: DMS.23 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.16: 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

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

EDO.5: 6 residues within 4Å: Chain A: K.228, A.231, D.232 Chain B: S.206, Y.213 Ligands: EDO.18 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.228 Water bridges: A:D.232, A:D.232, B:K.207 EDO.6: 7 residues within 4Å: Chain A: S.201, G.202, L.203, S.206, Y.213 Chain B: K.228 Ligands: EDO.17 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: 1 residues within 4Å: Chain A: K.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.103 EDO.17: 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 A, 1 interactions with chain B Water bridges: A:K.207 Hydrogen bonds: B:K.228 EDO.18: 7 residues within 4Å: Chain A: K.228 Chain B: S.201, G.202, L.203, S.206, Y.213 Ligands: EDO.5 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.228, B:G.202 EDO.19: 1 residues within 4Å: Chain B: K.103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.103

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 2 residues within 4Å: Chain A: E.144, G.145 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: E.144, G.145 Ligand excluded by PLIP

4 x CA: CALCIUM ION(Non-covalent)

CA.9: 6 residues within 4Å: Chain A: Q.211, D.214, D.216, D.217 Chain B: D.183 Ligands: CA.10 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.10: 6 residues within 4Å: Chain A: D.214, D.216 Chain B: L.182, D.183 Ligands: PHQ-VAL-ALA-ASP-CF0.1, CA.9 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.11 CA.21: 6 residues within 4Å: Chain A: D.183 Chain B: Q.211, D.214, D.216, D.217 Ligands: CA.22 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.22: 6 residues within 4Å: Chain A: L.182, D.183 Chain B: D.214, D.216 Ligands: PHQ-VAL-ALA-ASP-CF0.13, CA.21 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.21

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

DMS.11: 3 residues within 4Å: Chain A: Y.74, N.75 Ligands: GLA-FUC-GLA.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.75 DMS.23: 3 residues within 4Å: Chain B: Y.74, N.75 Ligands: GLA-FUC-GLA.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.75

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

NA.12: 2 residues within 4Å: Chain A: P.204, Q.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.204 NA.24: 2 residues within 4Å: Chain B: P.204, Q.276 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cordara, G. et al., An Unusual Member of the Papain Superfamily: Mapping the Catalytic Cleft of the Marasmius oreades agglutinin (MOA) with a Caspase Inhibitor. Plos One (2016)

Release Date

2016-03-02

Peptides

Agglutinin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Agglutinin

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