SMTL ID : 7aq1.1

Crystal structure of human mature meprin beta in complex with the specific inhibitor MWT-S-270

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

2 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: 7 residues within 4Å: Chain A: E.6, R.9, H.12, L.191, Y.192, N.193 Chain B: H.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.6 NAG-NAG.3: 8 residues within 4Å: Chain A: H.12 Chain B: E.6, R.9, W.10, H.12, L.191, Y.192, N.193 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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.2: 16 residues within 4Å: Chain A: P.391, Y.393, S.395, K.396, G.397, A.399, I.419, S.420, G.421, A.422, N.423, Q.426, L.427, F.484, N.486, T.488 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.391, A:F.484 Hydrogen bonds: A:Y.393

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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.4: 16 residues within 4Å: Chain B: P.391, Y.393, S.395, K.396, G.397, A.399, I.419, S.420, G.421, 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:P.391, B:I.419, B:F.484

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: H.91, H.95, H.101, Y.150 Ligands: RUE.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.91, A:H.95, A:H.101 ZN.16: 5 residues within 4Å: Chain B: H.91, H.95, H.101, Y.150 Ligands: RUE.19 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.91, B:H.95, B:H.101

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 9 residues within 4Å: Chain A: G.175, Q.176, R.177, M.178, N.453, F.501, I.502, T.503, R.506 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.175, A:R.177, A:T.503, A:R.506 EDO.7: 5 residues within 4Å: Chain A: E.35, R.38, R.275, F.277, R.365 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.275, A:R.365, A:R.365 EDO.8: 11 residues within 4Å: Chain A: K.40, D.179, F.180, S.181, D.182, L.185, R.448, Q.449, R.450, M.451, R.510 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.40, A:D.179 Water bridges: A:Q.449, A:R.510 EDO.17: 9 residues within 4Å: Chain B: G.175, Q.176, R.177, M.178, N.453, F.501, I.502, T.503, R.506 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.177, B:T.503, B:R.506 EDO.18: 8 residues within 4Å: Chain A: L.208, N.210, C.212 Chain B: V.140, P.141, Y.142, D.143, S.183 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:P.141, B:S.183, A:N.210 Water bridges: A:C.212

2 x RUE: 3-[[(3-Carboxyphenyl)methyl-[2-(hydroxyamino)-2-oxoethyl]amino]methyl]benzoic acid(Non-covalent)

RUE.9: 17 residues within 4Å: Chain A: S.61, G.62, C.63, W.64, S.65, H.91, E.92, H.95, H.101, R.123, N.126, Y.150, S.151, A.154, F.155, R.177 Ligands: ZN.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.155 Hydrogen bonds: A:C.63, A:S.151, A:S.151, A:R.177 Water bridges: A:E.92 Salt bridges: A:R.123 pi-Stacking: A:Y.150 RUE.19: 16 residues within 4Å: Chain B: S.61, G.62, C.63, W.64, S.65, H.91, E.92, H.95, H.101, N.126, Y.150, S.151, A.154, F.155, R.177 Ligands: ZN.16 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.64, B:F.155 Hydrogen bonds: B:C.63, B:C.63, B:S.151, B:S.151, B:R.177 Water bridges: B:S.65, B:S.65 pi-Stacking: B:Y.150

4 x CA: CALCIUM ION(Non-covalent)

CA.10: 7 residues within 4Å: Chain A: S.205, F.206, E.207, D.237, S.239, F.249, D.357 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.207, A:D.237, A:S.239, A:F.249, A:D.357 CA.11: 5 residues within 4Å: Chain A: S.217, D.220, A.222, D.223, V.265 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.217, A:D.220, A:D.220, A:A.222, A:D.223 CA.20: 7 residues within 4Å: Chain B: S.205, F.206, E.207, D.237, S.239, F.249, D.357 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.207, B:D.237, B:S.239, B:F.249, B:D.357 CA.21: 5 residues within 4Å: Chain B: S.217, S.218, D.220, A.222, D.223 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.217, B:D.220, B:A.222, B:D.223, H2O.10

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

CL.12: 4 residues within 4Å: Chain A: Q.281, L.441, I.447, R.450 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain B: Q.281, L.441, I.447, R.450 Ligand excluded by PLIP

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

NAG.13: 3 residues within 4Å: Chain A: L.120, S.121, N.157 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.120 Hydrogen bonds: A:S.121, A:S.121, A:N.157 NAG.14: 5 residues within 4Å: Chain A: Q.378, F.379, S.382, P.383, N.384 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.378 NAG.15: 4 residues within 4Å: Chain A: S.528, H.529, N.531, S.532 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.532 NAG.23: 3 residues within 4Å: Chain B: L.120, S.121, N.157 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.120 Hydrogen bonds: B:S.121, B:N.157 NAG.24: 4 residues within 4Å: Chain B: Q.378, F.379, S.382, N.384 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.378, B:N.384

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Linnert, M. et al., Structure and Dynamics of Meprin beta in Complex with a Hydroxamate-Based Inhibitor. Int J Mol Sci (2021)

Release Date

2021-03-03

Peptides

Meprin B subunit beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Meprin B subunit beta