SMTL ID : 7uai.1

Meprin alpha helix in complex with fetuin-B

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-mer

Ligands

3 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.1: 2 residues within 4Å: Chain A: Y.244, N.245 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.6: 1 residues within 4Å: Chain C: N.245 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.12: 4 residues within 4Å: Chain E: R.61, M.243, Y.244, N.245 No protein-ligand interaction detected (PLIP)

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.2: 2 residues within 4Å: Chain A: N.209, V.212 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: Y.106, I.108, F.112, G.125, N.127 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 9 residues within 4Å: Chain C: Y.106, I.108, F.112, G.125, Q.126, N.127 Chain F: G.105, M.106, I.108 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:M.106, F:M.106 NAG-NAG.7: 2 residues within 4Å: Chain C: N.209, V.212 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain D: Y.106, F.112, G.125, Q.126, N.127 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain D: N.209, V.212 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain E: N.209, S.211, V.212 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 7 residues within 4Å: Chain B: G.105, M.106, I.108 Chain E: F.112, G.125, Q.126, N.127 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.106

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.3: 10 residues within 4Å: Chain A: T.338, G.339, S.340, P.341, D.371, H.373, N.401, S.402, T.403, G.404 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.8: 9 residues within 4Å: Chain C: T.338, G.339, S.340, P.341, D.371, H.373, N.401, S.402, 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.11: 10 residues within 4Å: Chain D: T.338, G.339, S.340, P.341, D.371, H.373, N.401, S.402, T.403, G.404 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.371, D:D.371, D:T.338, D:H.373, D:T.403, D:T.403, D:G.404 NAG-NAG-BMA-FUC.14: 9 residues within 4Å: Chain E: T.338, G.339, S.340, P.341, D.371, H.373, N.401, S.402, T.403 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:D.371, E:D.371, E:G.339, E:H.373, E:T.403, E:T.403, E:G.404

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: 5 residues within 4Å: Chain A: T.257, D.288, T.290, Y.300, D.409 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.257, A:D.288, A:T.290, A:Y.300, A:D.409 CA.21: 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.23: 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:D.288, C:T.290, C:Y.300, C:D.409 CA.25: 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.27: 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:T.290, D:Y.300, D:D.409, D:D.409 CA.29: 4 residues within 4Å: Chain E: G.269, D.272, T.274, D.275 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:G.269, E:D.272, E:D.272, E:T.274, E:D.275 CA.30: 6 residues within 4Å: Chain E: T.257, E.259, D.288, T.290, Y.300, D.409 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:T.257, E:D.288, E:T.290, E:Y.300, E:D.409

4 x ZN: ZINC ION(Non-covalent)

ZN.17: 4 residues within 4Å: Chain A: H.142, E.143, H.146, H.152 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.142, A:H.146, A:H.152 ZN.20: 5 residues within 4Å: Chain B: D.153 Chain E: H.142, E.143, H.146, H.152 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain E Metal complexes: B:D.153, B:D.153, E:H.142, E:H.146, E:H.152 ZN.22: 5 residues within 4Å: Chain C: H.142, E.143, H.146, H.152 Chain F: D.153 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.142, C:H.146, C:H.152 ZN.26: 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: N.427, Q.430 No protein-ligand interaction detected (PLIP) NAG.24: 2 residues within 4Å: Chain C: N.427, Q.430 No protein-ligand interaction detected (PLIP) NAG.28: 3 residues within 4Å: Chain D: R.426, N.427, Q.430 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:R.426 NAG.31: 3 residues within 4Å: Chain E: R.426, N.427, Q.430 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:R.426

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: ACDE
Fetuin-B: BF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
B

D
C

E
D

B
A

F
H

Meprin A subunit alpha

Fetuin-B

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