SMTL ID : 6tav.1

Crystal structure of endopeptidase-induced alpha2-macroglobulin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.20 Å

Oligo State

homo-tetramer

Ligands

5 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 5 residues within 4Å: Chain A: V.25, N.55, E.56, T.111, Q.112 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.3: 2 residues within 4Å: Chain A: V.383, N.396 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.6: 5 residues within 4Å: Chain B: K.28, P.29, N.55, T.111, Q.112 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.11: 5 residues within 4Å: Chain B: D.988, N.991, E.992, Y.1055, R.1271 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.1271, B:R.1271 NAG-NAG-BMA-MAN.18: 5 residues within 4Å: Chain D: N.991, E.992, Q.994, Y.1055, R.1271 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.1271

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

NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: N.70, S.72 Chain C: T.1115, T.1117 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 5 residues within 4Å: Chain A: D.988, N.991, E.992, Y.1055, R.1271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.1271, A:R.1271, A:R.1271 NAG-NAG-BMA.9: 2 residues within 4Å: Chain B: Y.394, N.396 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 5 residues within 4Å: Chain C: D.988, N.991, E.992, Y.1055, R.1271 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.1271

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

NAG-NAG.4: 4 residues within 4Å: Chain A: Y.734, F.735, N.867, N.869 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.735 NAG-NAG.7: 3 residues within 4Å: Chain B: N.70, S.72 Chain D: T.1115 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: N.247, Q.303 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.867, N.869 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.410 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain C: N.867, N.869 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain D: G.27, K.28, P.29, N.55, T.111 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain D: V.383, F.385, N.396 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain D: N.867, N.869 No protein-ligand interaction detected (PLIP)

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

NAG.19: 4 residues within 4Å: Chain A: N.247, Y.301, Q.302, Q.303 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.303 Hydrogen bonds: A:Q.303 NAG.20: 2 residues within 4Å: Chain A: N.410, T.412 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain A: S.1372, N.1424 No protein-ligand interaction detected (PLIP) NAG.22: 2 residues within 4Å: Chain B: N.410, T.412 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.412 NAG.23: 4 residues within 4Å: Chain C: P.29, N.55, T.111, Q.112 No protein-ligand interaction detected (PLIP) NAG.24: 3 residues within 4Å: Chain A: T.1117 Chain C: N.70, S.72 No protein-ligand interaction detected (PLIP) NAG.25: 2 residues within 4Å: Chain C: N.247, Q.303 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.303 NAG.26: 3 residues within 4Å: Chain C: V.383, F.385, N.396 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.385 Hydrogen bonds: C:N.396 NAG.27: 3 residues within 4Å: Chain D: N.70, R.71, S.72 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.70 NAG.28: 1 residues within 4Å: Chain D: N.247 No protein-ligand interaction detected (PLIP) NAG.29: 1 residues within 4Å: Chain D: N.410 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luque, D. et al., Cryo-EM structures shows the mechanistic basis of pan-peptidase inhibition by human alpha2-macroglobulin. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2021-05-12

Peptides

Alpha-2-macroglobulin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Alpha-2-macroglobulin

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