SMTL ID : 4gwm.1

Crystal structure of human promeprin beta

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 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.1: 8 residues within 4Å: Chain A: E.45, H.51, L.230, N.232 Chain B: H.51, Y.231, N.232 Ligands: NAG-NAG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.45 NAG-NAG-BMA.5: 3 residues within 4Å: Chain A: L.159, S.160, N.196 No protein-ligand interaction detected (PLIP)

1 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.337, E.339, N.348, T.350, V.352, K.371, V.372 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.337, A:V.352 Hydrogen bonds: A:K.371 Water bridges: A:K.371

2 x NAG- FUC: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.3: 3 residues within 4Å: Chain A: Q.417, S.421, N.423 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.417, A:N.423 NAG-FUC.10: 2 residues within 4Å: Chain B: R.413, N.414 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.413 Hydrogen bonds: B:N.414

2 x NAG- NAG- BMA- 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-(1-3)]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.4: 12 residues within 4Å: Chain A: P.430, Y.432, S.434, K.435, G.436, A.461, N.462, Q.465, L.466, F.523, N.525, T.527 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.430, A:F.523 Hydrogen bonds: A:Y.432 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.9: 12 residues within 4Å: Chain B: P.430, Y.432, S.434, K.435, G.436, A.461, N.462, Q.465, L.466, F.523, N.525, T.527 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.430, B:F.523 Hydrogen bonds: B:Y.432, B:Y.432

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

NAG-NAG.6: 8 residues within 4Å: Chain A: H.51, Y.231, N.232 Chain B: E.45, H.51, L.230, N.232 Ligands: NAG-NAG-BMA.1 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:H.51 Hydrogen bonds: B:E.45

1 x NAG- NAG- BMA- MAN- FUC- FUC: alpha-D-mannopyranose-(1-3)-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.7: 7 residues within 4Å: Chain B: I.337, E.339, N.348, T.350, V.352, K.371, V.372 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.337, B:V.352 Hydrogen bonds: B:K.371 Water bridges: B:K.371

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

NAG-FUC-NAG-FUC.8: 5 residues within 4Å: Chain B: Q.417, F.418, S.421, P.422, N.423 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.11: 5 residues within 4Å: Chain A: F.16, D.30, H.130, H.134, H.140 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.30, A:D.30, A:H.130, A:H.134, A:H.140 ZN.17: 4 residues within 4Å: Chain B: D.30, H.130, H.134, H.140 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.30, B:D.30, B:H.130, B:H.134, B:H.140

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

NA.12: 6 residues within 4Å: Chain A: S.244, E.246, D.276, S.278, F.288, D.396 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.244, A:S.278, A:F.288 NA.18: 6 residues within 4Å: Chain B: S.244, E.246, D.276, S.278, F.288, D.396 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.246, B:D.276, B:F.288

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

NAG.13: 2 residues within 4Å: Chain A: R.413, N.414 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.413 Hydrogen bonds: A:N.414 NAG.19: 3 residues within 4Å: Chain B: L.159, S.160, N.196 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.159 Hydrogen bonds: B:S.160

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.14: 4 residues within 4Å: Chain A: S.244, F.245, E.246, C.251 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain A: V.68, N.71, I.125, Q.493, S.495 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: V.68, N.71, I.125, Q.493, S.495 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: P.50, N.92, N.108, R.110 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: Q.320, L.480, R.489 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 4 residues within 4Å: Chain A: G.258, D.259, N.260, N.298 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.258, A:D.259, A:N.298

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
B

Meprin A subunit beta