SMTL ID : 7cbk.1

Structure of Human Neutrophil Elastase Ecotin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-mer

Ligands

3 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.1: 6 residues within 4Å: Chain C: R.78, V.80, R.81, V.98, A.100, N.124 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:R.81, C:V.98 Hydrogen bonds: C:R.81 NAG-NAG-FUC.2: 10 residues within 4Å: Chain C: R.34, W.41, Q.150, C.151, L.152, N.173, V.207, C.208, N.209, G.210 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.41, C:V.207 Hydrogen bonds: C:Q.150, C:N.209, C:G.210 NAG-NAG-FUC.3: 9 residues within 4Å: Chain D: R.34, Q.150, C.151, L.152, N.173, V.207, C.208, N.209, G.210 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.150, D:N.209, D:G.210

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain C: R.182, R.183, S.184 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.183, C:S.184 Water bridges: C:S.184

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

SO4.5: 2 residues within 4Å: Chain C: N.162, R.163 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.163 SO4.8: 2 residues within 4Å: Chain D: N.162, R.163 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.162 Water bridges: D:N.162 Salt bridges: D:R.163

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain C: G.196, V.197, V.219, C.223, D.230 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:V.197, C:C.223, C:D.230

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

NAG.7: 4 residues within 4Å: Chain D: R.81, V.98, A.100, N.124 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jobichen, C. et al., Structural Basis for the Inhibition Mechanism of Ecotin against Neutrophil Elastase by Targeting the Active Site and Secondary Binding Site. Biochemistry (2020)

Release Date

2020-08-12

Peptides

Ecotin: AB
Neutrophil elastase: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
B

Ecotin

Neutrophil elastase

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