SMTL ID : 4gwn.1

Crystal structure of human mature meprin beta

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

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: 4 residues within 4Å: Chain A: E.6, Q.190, N.193 Chain B: S.195 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: L.120, S.121, N.157 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: S.195 Chain B: E.6, Q.190, N.193 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: L.120, S.121, N.157 No protein-ligand interaction detected (PLIP)

2 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.2: 7 residues within 4Å: Chain A: I.298, E.300, D.304, N.309, T.311, K.332, V.333 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.12: 7 residues within 4Å: Chain B: I.298, E.300, D.304, N.309, T.311, K.332, V.333 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.298 Hydrogen bonds: B:K.332

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: 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)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]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-MAN-MAN-MAN-MAN.3: 14 residues within 4Å: Chain A: P.391, Y.393, S.395, K.396, G.397, I.419, S.420, A.422, N.423, Q.426, L.427, F.484, N.486, T.488 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.419, A:F.484 Hydrogen bonds: A:Y.393, A:Y.393 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.13: 14 residues within 4Å: Chain B: P.391, Y.393, S.395, K.396, G.397, I.419, S.420, A.422, N.423, Q.426, L.427, F.484, N.486, T.488 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.419, B:F.484 Hydrogen bonds: B:Y.393

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: 4 residues within 4Å: Chain A: R.374, N.375, Q.378 Ligands: NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.15: 4 residues within 4Å: Chain B: R.374, N.375, Q.378 Ligands: NAG.18 No protein-ligand interaction detected (PLIP)

2 x CD: CADMIUM ION(Non-covalent)

CD.6: 4 residues within 4Å: Chain A: H.91, E.92, H.95, H.101 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.91, A:H.95, A:H.101 CD.16: 4 residues within 4Å: Chain B: H.91, E.92, H.95, H.101 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.91, B:H.95, B:H.101

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

NA.7: 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:S.239, A:F.249 NA.17: 6 residues within 4Å: Chain B: S.205, E.207, D.237, S.239, F.249, D.357 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.237, B:D.237, B:S.239, B:F.249

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

NAG.8: 5 residues within 4Å: Chain A: Q.378, S.382, P.383, N.384 Ligands: NAG-NAG-FUC.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.383 NAG.9: 1 residues within 4Å: Chain A: N.531 No protein-ligand interaction detected (PLIP) NAG.18: 5 residues within 4Å: Chain B: Q.378, S.382, P.383, N.384 Ligands: NAG-NAG-FUC.15 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.383 NAG.19: 1 residues within 4Å: Chain B: N.531 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 2 residues within 4Å: Chain A: F.155, R.177 No protein-ligand interaction detected (PLIP) GOL.20: 2 residues within 4Å: Chain B: F.155, R.177 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arolas, J.L. et al., Structural basis for the sheddase function of human meprin beta metalloproteinase at the plasma membrane. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-09-19

Peptides

Meprin A subunit beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Meprin A subunit beta