SMTL ID : 7z6t.1

Aspergillus clavatus M36 protease without the propeptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[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.1: 3 residues within 4Å: Chain A: N.72, S.74 Ligands: DNO-BMA.2 No protein-ligand interaction detected (PLIP)

1 x DNO- BMA: beta-D-mannopyranose-(1-3)-D-mannose(Non-functional Binders)

DNO-BMA.2: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP)

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

EDO.3: 3 residues within 4Å: Chain A: A.233, K.234, D.235 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.234, A:K.234, A:D.235 EDO.4: 3 residues within 4Å: Chain A: S.54, P.56, H.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.54 Water bridges: A:H.66 EDO.5: 4 residues within 4Å: Chain A: R.232, N.291, K.360, A.361 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.291, A:K.360 Water bridges: A:R.232, A:K.360 EDO.6: 4 residues within 4Å: Chain A: D.272, S.273, V.274, H.275 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.274, A:H.275, A:H.275 EDO.7: 3 residues within 4Å: Chain A: P.13, T.14, P.81 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.241 EDO.8: 6 residues within 4Å: Chain A: G.9, I.224, V.300, S.301, K.315, Y.316 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.315 EDO.9: 3 residues within 4Å: Chain A: P.24, W.25, D.26 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.26 EDO.10: 2 residues within 4Å: Chain A: N.123, N.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.123 Water bridges: A:N.125, A:N.125 EDO.11: 3 residues within 4Å: Chain A: K.40, P.43, R.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.40, A:R.69 Water bridges: A:R.69 EDO.12: 5 residues within 4Å: Chain A: S.87, S.88, Y.89, I.90, D.91 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.91, A:D.91 Water bridges: A:D.91, A:A.92 EDO.13: 5 residues within 4Å: Chain A: L.204, S.205, T.206, I.207, G.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.204 EDO.14: 3 residues within 4Å: Chain A: A.363, K.364, N.382 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.382 EDO.15: 4 residues within 4Å: Chain A: H.66, P.68, R.69, D.91 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.69, A:R.69, A:D.91

1 x ZN: ZINC ION(Non-covalent)

ZN.16: 3 residues within 4Å: Chain A: H.184, H.188, E.214 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.184, A:H.188, A:E.214

1 x CA: CALCIUM ION(Non-covalent)

CA.17: 5 residues within 4Å: Chain A: N.119, R.130, D.133, D.155, R.193 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.119, A:R.130, A:D.133, H2O.4, H2O.6

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

SO4.18: 3 residues within 4Å: Chain A: D.340, L.343, D.344 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.344 Water bridges: A:D.340 Salt bridges: A:K.347 SO4.19: 3 residues within 4Å: Chain A: R.130, G.131, N.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.131, A:G.131 Water bridges: A:N.132, A:N.132 SO4.20: 3 residues within 4Å: Chain A: I.249, R.250, E.251 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.251 SO4.21: 5 residues within 4Å: Chain A: S.36, G.38, T.39, K.40, K.41 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.36, A:K.41 Water bridges: A:K.41 SO4.22: 2 residues within 4Å: Chain A: R.46, I.63 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.46

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

NA.23: 4 residues within 4Å: Chain A: E.31, E.115, E.121, Q.127 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.31, A:N.48, A:E.115, A:Q.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilkens, C. et al., Aspergillus clavatus M36 protease without the propeptide. To Be Published

Release Date

2023-03-22

Peptides

Extracellular metalloproteinase mep: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Extracellular metalloproteinase mep