SMTL ID : 7auw.1

Inhibitory complex of human meprin beta with mouse fetuin-B.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-2-mer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- FUC- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC-FUC.1: 7 residues within 4Å: Chain A: D.117, L.120, S.121, N.157 Chain B: S.164, N.165, P.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.121 NAG-NAG-BMA-MAN-MAN-FUC-FUC.3: 7 residues within 4Å: Chain A: I.298, E.300, N.309, T.311, K.332, V.333, T.334 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.298 Hydrogen bonds: A:K.332 NAG-NAG-BMA-MAN-MAN-FUC-FUC.9: 7 residues within 4Å: Chain C: D.117, L.120, S.121, N.157 Chain D: S.164, N.165, P.166 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.121 NAG-NAG-BMA-MAN-MAN-FUC-FUC.11: 8 residues within 4Å: Chain C: I.298, E.300, N.309, T.311, V.313, K.332, V.333, T.334 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.298, C:T.311, C:V.313 Hydrogen bonds: C:K.332

3 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: 5 residues within 4Å: Chain A: E.6, H.12, L.191, Y.192, N.193 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 5 residues within 4Å: Chain C: E.6, H.12, L.191, Y.192, N.193 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 1 residues within 4Å: Chain D: N.40 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- FUC- FUC: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC-FUC.4: 3 residues within 4Å: Chain A: N.375, Q.378 Ligands: NAG-NAG-FUC.5 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC-FUC.12: 3 residues within 4Å: Chain C: N.375, Q.378 Ligands: NAG-NAG-FUC.13 No protein-ligand interaction detected (PLIP)

2 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.5: 5 residues within 4Å: Chain A: S.382, P.383, N.384 Ligands: NAG-NAG-BMA-MAN-FUC-FUC.4, NAG-NAG-BMA-MAN-FUC-FUC.4 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.13: 5 residues within 4Å: Chain C: S.382, P.383, N.384 Ligands: NAG-NAG-BMA-MAN-FUC-FUC.12, NAG-NAG-BMA-MAN-FUC-FUC.12 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN- GLC- MAN- MAN- MAN- MAN- MAN: alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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-MAN-MAN-GLC-MAN-MAN-MAN-MAN-MAN.6: 12 residues within 4Å: Chain A: P.391, Y.393, S.395, K.396, G.397, A.422, N.423, Q.426, L.427, F.484, N.486, T.488 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.396, A:Y.393 Hydrophobic interactions: A:P.391, A:F.484 NAG-NAG-BMA-MAN-MAN-MAN-GLC-MAN-MAN-MAN-MAN-MAN.14: 12 residues within 4Å: Chain C: P.391, Y.393, S.395, K.396, G.397, A.422, N.423, Q.426, L.427, F.484, N.486, T.488 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.396, C:Y.393, C:Y.393 Hydrophobic interactions: C:P.391, C:F.484

2 x NAG- FUC- FUC: alpha-L-fucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-FUC.7: 5 residues within 4Å: Chain A: D.20, L.22, M.24, N.531, S.532 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.531, A:S.532, A:D.20 NAG-FUC-FUC.15: 5 residues within 4Å: Chain C: D.20, L.22, M.24, N.531, S.532 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.531, C:S.532, C:D.20

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.8: 4 residues within 4Å: Chain B: N.139, Q.333, L.334, D.335 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.17: 5 residues within 4Å: Chain D: N.139, G.305, Q.333, L.334, D.335 No protein-ligand interaction detected (PLIP)

2 x NA: SODIUM ION(Non-functional Binders)

NA.18: 6 residues within 4Å: Chain A: S.205, E.207, D.237, S.239, F.249, D.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.239, A:F.249, A:F.249 NA.22: 6 residues within 4Å: Chain C: S.205, E.207, D.237, S.239, F.249, D.357 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.237, C:S.239, C:F.249

2 x ZN: ZINC ION(Non-covalent)

ZN.19: 4 residues within 4Å: Chain A: H.91, H.95, H.101 Chain B: D.156 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:D.156, B:D.156, A:H.91, A:H.95, A:H.101 ZN.23: 4 residues within 4Å: Chain C: H.91, H.95, H.101 Chain D: D.156 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Metal complexes: D:D.156, D:D.156, C:H.91, C:H.95, C:H.101

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.20: 3 residues within 4Å: Chain A: S.151, R.177 Chain B: W.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.151, A:S.151 Salt bridges: A:R.177 SO4.24: 4 residues within 4Å: Chain C: Y.150, S.151, R.177 Chain D: W.200 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:W.200, C:S.151, C:S.151, C:G.175 Salt bridges: C:R.177

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

NAG.21: 1 residues within 4Å: Chain B: N.40 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eckhard, U. et al., The crystal structure of a 250-kDa heterotetrameric particle explains inhibition of sheddase meprin beta by endogenous fetuin-B. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-04-14

Peptides

Meprin A subunit beta: AC
Fetuin-B: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Meprin A subunit beta

Fetuin-B