SMTL ID : 5d63.1

MOA-Z-VAD-fmk inhibitor complex, direct/inverted dual orientation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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

PHQ-VAL-ALA-ASP-CF0.1: 14 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, D.183 Ligands: CA.14 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.249 Hydrogen bonds: A:C.215, A:D.216, A:A.256, A:A.256 Water bridges: A:Y.289, B:D.183 PHQ-VAL-ALA-ASP-CF0.16: 14 residues within 4Å: Chain A: I.181, L.182, D.183 Chain B: W.208, D.214, C.215, D.216, V.249, G.253, A.256, H.257, A.258, Y.289 Ligands: CA.29 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.249 Hydrogen bonds: B:D.214, B:C.215, B:A.256 Water bridges: B:H.257

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 8 PLIP interactions: 8 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 Salt bridges: A:H.45 Water bridges: A:D.20, A:W.35, A:N.43, A:W.44, A:D.131 GAL-FUC-GLA.17: 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 10 PLIP interactions: 10 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, B:D.131

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.9 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.18: 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.24 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.19: 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: 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.6: 7 residues within 4Å: Chain A: S.201, G.202, L.203, S.206, Y.213 Chain B: K.228 Ligands: EDO.5 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: 6 residues within 4Å: Chain A: P.52, I.53, V.56, D.58, T.59, F.60 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.53, A:I.53, A:D.58 Water bridges: A:S.2, A:L.3 EDO.20: 6 residues within 4Å: Chain A: K.228, A.231, D.232 Chain B: S.206, Y.213 Ligands: EDO.21 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.21: 7 residues within 4Å: Chain A: K.228 Chain B: S.201, G.202, L.203, S.206, Y.213 Ligands: EDO.20 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.228, B:G.202 EDO.22: 6 residues within 4Å: Chain B: P.52, I.53, V.56, D.58, T.59, F.60 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.53, B:I.53, B:D.58 Water bridges: B:S.2, B:L.3

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

DMS.8: 1 residues within 4Å: Chain A: K.199 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.199 DMS.9: 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: 1 residues within 4Å: Chain B: K.199 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.199 DMS.24: 3 residues within 4Å: Chain B: Y.74, N.75 Ligands: GLA-FUC-GLA.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.75

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

CL.10: 3 residues within 4Å: Chain A: G.127, D.128, S.129 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: E.144, G.145 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: L.49, E.51, A.91, N.237 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain B: G.127, D.128, S.129 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: E.144, G.145 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain B: L.49, E.51, A.91, N.237 Ligand excluded by PLIP

4 x CA: CALCIUM ION(Non-covalent)

CA.13: 6 residues within 4Å: Chain A: Q.211, D.214, D.216, D.217 Chain B: D.183 Ligands: CA.14 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Metal complexes: B:D.183, A:Q.211, A:D.214, A:D.216, A:D.217 CA.14: 6 residues within 4Å: Chain A: D.214, D.216 Chain B: L.182, D.183 Ligands: PHQ-VAL-ALA-ASP-CF0.1, CA.13 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.28: 6 residues within 4Å: Chain A: D.183 Chain B: Q.211, D.214, D.216, D.217 Ligands: CA.29 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.29: 6 residues within 4Å: Chain A: L.182, D.183 Chain B: D.214, D.216 Ligands: PHQ-VAL-ALA-ASP-CF0.16, CA.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.22

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

NA.15: 1 residues within 4Å: Chain A: Q.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.204 NA.30: 1 residues within 4Å: Chain B: Q.276 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.276

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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