SMTL ID : 7uab.1

Human pro-meprin alpha (zymogen state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

7 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: Q.49, Q.110, F.112, E.118, G.125, N.127 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: G.125, Q.126, N.127 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain C: Y.106, I.108, F.112, E.118, G.125, Q.126, N.127 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: N.209, S.211 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain D: N.209, S.211 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain D: N.427 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain D: F.112, W.116, N.127 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-FUC.2: 7 residues within 4Å: Chain A: T.338, G.339, D.371, H.373, D.398, N.401, T.403 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.371, A:D.371, A:H.373 NAG-NAG-FUC.4: 8 residues within 4Å: Chain B: T.338, G.339, P.341, D.371, H.373, D.398, N.401, T.403 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.371, B:D.371 NAG-NAG-FUC.6: 11 residues within 4Å: Chain C: T.338, G.339, S.340, P.341, S.342, D.371, H.373, D.398, N.401, S.402, T.403 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.371, C:D.371, C:T.338 NAG-NAG-FUC.10: 11 residues within 4Å: Chain D: T.338, G.339, S.340, P.341, S.342, D.371, H.373, D.398, N.401, S.402, 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 Hydrophobic interactions: D:T.403

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

NAG.12: 3 residues within 4Å: Chain A: R.426, N.427, Q.430 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.426 Hydrogen bonds: A:Q.430 NAG.13: 2 residues within 4Å: Chain A: N.209, S.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.211 NAG.17: 3 residues within 4Å: Chain B: N.209, S.211, V.212 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.211 NAG.18: 5 residues within 4Å: Chain B: N.374, R.426, N.427, N.571, D.573 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.374, B:N.427 NAG.21: 5 residues within 4Å: Chain C: R.61, W.62, M.243, Y.244, N.245 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:R.61, C:Y.244 Hydrogen bonds: C:R.61, C:M.243 NAG.22: 2 residues within 4Å: Chain C: R.426, N.427 No protein-ligand interaction detected (PLIP) NAG.26: 3 residues within 4Å: Chain D: M.243, Y.244, N.245 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.244 Hydrogen bonds: D:M.243, D:N.245

7 x CA: CALCIUM ION(Non-covalent)

CA.14: 3 residues within 4Å: Chain A: D.272, T.274, D.275 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.272, A:D.272, A:T.274, A:D.275 CA.16: 5 residues within 4Å: Chain A: T.257, E.259, 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.20: 5 residues within 4Å: Chain B: T.257, E.259, 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.23: 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.25: 5 residues within 4Å: Chain C: T.257, E.259, T.290, Y.300, D.409 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:T.257, C:E.259, C:T.290, C:Y.300, C:D.409 CA.27: 4 residues within 4Å: Chain D: G.269, D.272, T.274, D.275 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:G.269, D:D.272, D:D.272, D:T.274, D:D.275 CA.29: 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.15: 4 residues within 4Å: Chain A: D.45, H.142, H.146, H.152 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.45, A:D.45, A:H.142, A:H.146, A:H.152 ZN.19: 4 residues within 4Å: Chain B: D.45, H.142, H.146, H.152 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.45, B:D.45, B:H.142, B:H.146, B:H.152 ZN.24: 4 residues within 4Å: Chain C: D.45, H.142, H.146, H.152 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.45, C:D.45, C:H.142, C:H.146, C:H.152 ZN.28: 4 residues within 4Å: Chain D: D.45, H.142, H.146, H.152 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.45, D:D.45, D:H.142, D:H.146, D:H.152

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
A

B
D

C
E

D
H

Meprin A subunit alpha

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