SMTL ID : 4wvp.1 (1 other biounit)

Crystal structure of an activity-based probe HNE complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

monomer

Ligands

1 x BTN- 3V3- NLB- OMT- OIC- 3V2: BTN-3V3-NLB-OMT-OIC-3V2(Non-covalent)

BTN-3V3-NLB-OMT-OIC-3V2.1: 21 residues within 4Å: Chain A: H.41, Y.80, V.83, N.84, L.85, L.151, C.152, R.153, C.169, F.170, G.171, D.172, S.173, S.188, F.189, V.190, R.191, G.192, G.193, Y.199 Ligands: SO4.12 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.85, A:L.85, A:R.153, A:F.170, A:F.189, A:F.189, A:V.190, A:R.191 Hydrogen bonds: A:N.84, A:G.171, A:D.172, A:S.173, A:S.188, A:V.190, A:V.190, A:G.192 Water bridges: A:N.84

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

NAG-NAG-BMA-FUC.2: 9 residues within 4Å: Chain A: W.12, Q.121, C.122, L.123, N.144, V.178, C.179, N.180, G.181 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.12, A:V.178 Hydrogen bonds: A:Q.121, A:N.180, A:G.181

1 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.3: 6 residues within 4Å: Chain A: R.49, V.51, R.52, V.69, A.71, N.95 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.52, A:V.69 Hydrogen bonds: A:R.52 Water bridges: A:V.69

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

SO4.4: 7 residues within 4Å: Chain A: R.6, L.130, R.134, A.137, S.138, V.139, Q.141 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.138, A:V.139, A:Q.141 Water bridges: A:R.6, A:R.134, A:S.138, A:Q.141 Salt bridges: A:R.6, A:R.134 SO4.5: 4 residues within 4Å: Chain A: N.118, V.148, T.149, S.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.149, A:S.150, A:S.150 SO4.12: 2 residues within 4Å: Ligands: BTN-3V3-NLB-OMT-OIC-3V2.1, BTN-3V3-NLB-OMT-OIC-3V2.1 No protein-ligand interaction detected (PLIP)

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

EDO.6: 4 residues within 4Å: Chain A: E.77, N.78, G.79, Y.80 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.77, A:E.77, A:G.79, A:Y.80 Water bridges: A:E.77, A:N.78 EDO.7: 3 residues within 4Å: Chain A: R.153, R.154, S.155 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.154, A:S.155 Water bridges: A:S.155 EDO.8: 2 residues within 4Å: Chain A: R.62, R.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.62, A:R.63 EDO.9: 2 residues within 4Å: Chain A: N.101, A.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.102 EDO.10: 5 residues within 4Å: Chain A: R.6, A.7, P.9, H.58, V.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.7 Water bridges: A:R.6 EDO.11: 2 residues within 4Å: Chain A: Q.112, N.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.211, A:N.211 Water bridges: A:Q.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lechtenberg, B.C. et al., The Elastase-PK101 Structure: Mechanism of an Ultrasensitive Activity-based Probe Revealed. Acs Chem.Biol. (2015)

Release Date

2015-02-11

Peptides

Neutrophil elastase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

Neutrophil elastase

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