SMTL ID : 7uaf.1

Human meprin alpha inhibitory complex with compound 10d (N~3~,N~3~-bis[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-beta-alaninamide)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: Y.106, I.108, F.112, G.125, Q.126, N.127 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.209 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain B: N.209 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain B: Q.110, F.112, E.118, G.125, Q.126, N.127 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain C: Y.106, F.112, G.125, Q.126, N.127 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain C: N.209 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain D: Y.106, I.108, F.112, G.125, Q.126, N.127 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain D: N.209 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.2: 3 residues within 4Å: Chain A: M.243, Y.244, N.245 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.5: 3 residues within 4Å: Chain B: M.243, Y.244, N.245 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.4: 7 residues within 4Å: Chain A: T.338, G.339, P.341, D.371, H.373, N.401, T.403 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.371, A:D.371, A:T.338, A:H.373, A:T.403, A:T.403 NAG-NAG-BMA-FUC.7: 8 residues within 4Å: Chain B: T.338, G.339, P.341, D.371, H.373, N.401, S.402, T.403 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.371, B:D.371, B:T.338, B:H.373, B:T.403, B:T.403 NAG-NAG-BMA-FUC.11: 7 residues within 4Å: Chain C: T.338, G.339, P.341, D.371, H.373, N.401, T.403 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.371, C:D.371, C:T.338, C:H.373, C:T.403, C:T.403 NAG-NAG-BMA-FUC.14: 7 residues within 4Å: Chain D: T.338, G.339, P.341, D.371, H.373, N.401, T.403 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.371, D:D.371, D:T.338, D:H.373, D:T.403, D:T.403

4 x M6X: N~3~,N~3~-bis[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-beta-alaninamide(Covalent)(Non-covalent)

M6X.15: 14 residues within 4Å: Chain A: C.115, C.134, I.139, H.142, E.143, H.146, H.152, L.198, H.200, Y.201, F.206, Q.228, R.229 Ligands: ZN.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.139, A:Y.201, A:F.206 Hydrogen bonds: A:C.115 pi-Stacking: A:H.142 M6X.20: 17 residues within 4Å: Chain B: C.115, Q.132, G.133, C.134, I.139, H.142, E.143, H.146, H.152, N.177, L.198, H.200, Y.201, F.206, Q.228, R.229 Ligands: ZN.22 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.139, B:I.139, B:Y.201 Hydrogen bonds: B:C.115, B:Y.201 pi-Stacking: B:H.142 M6X.25: 15 residues within 4Å: Chain C: C.115, Q.132, G.133, I.139, H.142, E.143, H.146, L.198, H.200, Y.201, F.206, G.227, Q.228, R.229 Ligands: ZN.27 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.139, C:I.139, C:R.229 Hydrogen bonds: C:C.115 pi-Stacking: C:H.142 M6X.30: 12 residues within 4Å: Chain D: C.115, W.116, Q.132, G.133, C.134, A.138, I.139, E.143, L.198, F.206, Q.228, R.229 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.139, D:I.139, D:R.229 Hydrogen bonds: D:C.115 pi-Stacking: D:H.142

8 x CA: CALCIUM ION(Non-covalent)

CA.16: 4 residues within 4Å: Chain A: G.269, D.272, T.274, D.275 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.269, A:D.272, A:D.272, A:T.274, A:D.275 CA.18: 6 residues within 4Å: Chain A: T.257, E.259, D.288, T.290, Y.300, D.409 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.257, A:E.259, A:T.290, A:Y.300, A:D.409 CA.21: 4 residues within 4Å: Chain B: G.269, D.272, T.274, D.275 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:G.269, B:D.272, B:D.272, B:T.274, B:D.275 CA.23: 6 residues within 4Å: Chain B: T.257, E.259, D.288, T.290, Y.300, D.409 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.257, B:E.259, B:T.290, B:Y.300, B:D.409 CA.26: 4 residues within 4Å: Chain C: G.269, D.272, T.274, D.275 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.269, C:D.272, C:D.272, C:T.274, C:D.275 CA.28: 6 residues within 4Å: Chain C: T.257, E.259, D.288, T.290, Y.300, D.409 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:T.257, C:E.259, C:D.288, C:T.290, C:Y.300 CA.31: 4 residues within 4Å: Chain D: G.269, D.272, T.274, D.275 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:G.269, D:D.272, D:T.274, D:D.275 CA.33: 6 residues within 4Å: Chain D: T.257, E.259, D.288, T.290, Y.300, D.409 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:T.257, D:E.259, D:T.290, D:Y.300, D:D.409

4 x ZN: ZINC ION(Non-covalent)

ZN.17: 4 residues within 4Å: Chain A: H.142, H.146, H.152 Ligands: M6X.15 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.142, A:H.146, A:H.152 ZN.22: 4 residues within 4Å: Chain B: H.142, H.146, H.152 Ligands: M6X.20 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.142, B:H.146, B:H.152 ZN.27: 4 residues within 4Å: Chain C: H.142, H.146, H.152 Ligands: M6X.25 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.142, C:H.146, C:H.152 ZN.32: 3 residues within 4Å: Chain D: H.142, H.146, H.152 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.142, D:H.146, D:H.152

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.19: 2 residues within 4Å: Chain A: R.426, N.427 No protein-ligand interaction detected (PLIP) NAG.24: 2 residues within 4Å: Chain B: R.426, N.427 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.427 NAG.29: 2 residues within 4Å: Chain C: R.426, N.427 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:R.426 Hydrogen bonds: C:N.427 NAG.34: 2 residues within 4Å: Chain D: R.426, N.427 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.427

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bayly-Jones, C. et al., Helical ultrastructure of the metalloprotease meprin alpha in complex with a small molecule inhibitor. Nat Commun (2022)

Release Date

2022-11-02

Peptides

Meprin A subunit alpha: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
D

Meprin A subunit alpha

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