SMTL ID : 7o7s.1

(h-alpha2M)4 plasmin-activated II state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 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: 3 residues within 4Å: Chain A: N.867, N.869, P.902 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: N.867, V.868, N.869 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: N.867, N.869 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain D: E.245, N.247, Y.301, Q.302, Q.303 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.303

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: 8 residues within 4Å: Chain A: D.988, N.991, E.992, K.1001, A.1054, Y.1055, R.1271, T.1272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.1271, A:T.1272 NAG-NAG-BMA.4: 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.6: 4 residues within 4Å: Chain C: N.991, L.996, K.1001, Y.1055 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.1055 NAG-NAG-BMA.9: 3 residues within 4Å: Chain D: N.410, T.411, T.412 No protein-ligand interaction detected (PLIP)

1 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.8: 1 residues within 4Å: Chain D: N.396 No protein-ligand interaction detected (PLIP)

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

NAG.10: 4 residues within 4Å: Chain A: L.54, N.55, P.110, T.111 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.70, R.71 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: E.245, N.247, Q.303, K.375 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: V.383, I.384, F.385, N.396 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: Y.393, S.408, N.410 Ligand excluded by PLIP NAG.15: 6 residues within 4Å: Chain B: P.29, L.54, N.55, P.110, T.111, Q.112 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain B: E.65, N.70, S.72, F.74 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: E.245, N.247, Q.303 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: Y.394, S.395, N.396 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.410 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain C: L.54, N.55, T.111, Q.112, E.113 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: T.1115 Chain C: N.70 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain C: T.234, N.247, K.375 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: Y.394, S.395, N.396 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.410, T.412 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain D: P.29, N.55, E.56 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain D: N.70 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain D: N.867, V.868, N.869, P.902 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain D: N.991, E.992, G.1265, A.1266 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain D: V.1422, N.1424 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luque, D. et al., Cryo-EM structures show the mechanistic basis of pan-peptidase inhibition by human alpha 2 -macroglobulin. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-04-13

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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