SMTL ID : 4wvp.2 (1 other biounit)

Crystal structure of an activity-based probe HNE complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-trimer

Ligands

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

BTN-3V3-NLB-OMT-OIC-3V2.1: 35 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 Chain B: Y.199 Chain C: H.41, C.42, A.44, N.45, V.46, P.82 Ligands: SO4.12, BTN-3V3-NLB-OMT-OIC-3V2.13, BTN-3V3-NLB-OMT-OIC-3V2.13, SO4.24, BTN-3V3-NLB-OMT-OIC-3V2.25, BTN-3V3-NLB-OMT-OIC-3V2.25, BTN-3V3-NLB-OMT-OIC-3V2.25, SO4.36 20 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C 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, B:Y.199, B:Y.199 Water bridges: A:N.84, C:H.41 BTN-3V3-NLB-OMT-OIC-3V2.13: 35 residues within 4Å: Chain A: H.41, C.42, A.44, N.45, V.46, P.82 Chain B: 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 Chain C: Y.199 Ligands: BTN-3V3-NLB-OMT-OIC-3V2.1, BTN-3V3-NLB-OMT-OIC-3V2.1, BTN-3V3-NLB-OMT-OIC-3V2.1, SO4.12, SO4.24, BTN-3V3-NLB-OMT-OIC-3V2.25, BTN-3V3-NLB-OMT-OIC-3V2.25, SO4.36 20 PLIP interactions: 17 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:L.85, B:L.85, B:R.153, B:F.170, B:F.189, B:F.189, B:V.190, B:R.191 Hydrogen bonds: B:N.84, B:G.171, B:D.172, B:S.173, B:S.188, B:V.190, B:V.190, B:G.192, C:Y.199, C:Y.199 Water bridges: B:N.84, A:H.41 BTN-3V3-NLB-OMT-OIC-3V2.25: 35 residues within 4Å: Chain A: Y.199 Chain B: H.41, C.42, A.44, N.45, V.46, P.82 Chain C: 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: BTN-3V3-NLB-OMT-OIC-3V2.1, BTN-3V3-NLB-OMT-OIC-3V2.1, SO4.12, BTN-3V3-NLB-OMT-OIC-3V2.13, BTN-3V3-NLB-OMT-OIC-3V2.13, BTN-3V3-NLB-OMT-OIC-3V2.13, SO4.24, SO4.36 20 PLIP interactions: 17 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: C:L.85, C:L.85, C:R.153, C:F.170, C:F.189, C:F.189, C:V.190, C:R.191 Hydrogen bonds: C:N.84, C:G.171, C:D.172, C:S.173, C:S.188, C:V.190, C:V.190, C:G.192, A:Y.199, A:Y.199 Water bridges: C:N.84, B:H.41

3 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 NAG-NAG-BMA-FUC.14: 9 residues within 4Å: Chain B: 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 B Hydrophobic interactions: B:W.12, B:V.178 Hydrogen bonds: B:Q.121, B:N.180, B:G.181 NAG-NAG-BMA-FUC.26: 9 residues within 4Å: Chain C: 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 C Hydrophobic interactions: C:W.12, C:V.178 Hydrogen bonds: C:Q.121, C:N.180, C:G.181

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.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 NAG-NAG-FUC.15: 6 residues within 4Å: Chain B: R.49, V.51, R.52, V.69, A.71, N.95 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.52, B:V.69 Hydrogen bonds: B:R.52 Water bridges: B:V.69 NAG-NAG-FUC.27: 6 residues within 4Å: Chain C: R.49, V.51, R.52, V.69, A.71, N.95 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:R.52, C:V.69 Hydrogen bonds: C:R.52 Water bridges: C:V.69

9 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: 5 residues within 4Å: Chain A: N.118, V.148, T.149, S.150 Chain C: R.21 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.149, A:S.150, A:S.150 Salt bridges: C:R.21 SO4.12: 8 residues within 4Å: Ligands: BTN-3V3-NLB-OMT-OIC-3V2.1, BTN-3V3-NLB-OMT-OIC-3V2.1, BTN-3V3-NLB-OMT-OIC-3V2.13, BTN-3V3-NLB-OMT-OIC-3V2.13, SO4.24, BTN-3V3-NLB-OMT-OIC-3V2.25, BTN-3V3-NLB-OMT-OIC-3V2.25, SO4.36 No protein-ligand interaction detected (PLIP) SO4.16: 7 residues within 4Å: Chain B: R.6, L.130, R.134, A.137, S.138, V.139, Q.141 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.138, B:V.139, B:Q.141 Water bridges: B:R.6, B:R.134, B:S.138, B:Q.141 Salt bridges: B:R.6, B:R.134 SO4.17: 5 residues within 4Å: Chain A: R.21 Chain B: N.118, V.148, T.149, S.150 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.149, B:S.150, B:S.150 Salt bridges: A:R.21 SO4.24: 8 residues within 4Å: Ligands: BTN-3V3-NLB-OMT-OIC-3V2.1, BTN-3V3-NLB-OMT-OIC-3V2.1, SO4.12, BTN-3V3-NLB-OMT-OIC-3V2.13, BTN-3V3-NLB-OMT-OIC-3V2.13, BTN-3V3-NLB-OMT-OIC-3V2.25, BTN-3V3-NLB-OMT-OIC-3V2.25, SO4.36 No protein-ligand interaction detected (PLIP) SO4.28: 7 residues within 4Å: Chain C: R.6, L.130, R.134, A.137, S.138, V.139, Q.141 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.138, C:V.139, C:Q.141 Water bridges: C:R.6, C:R.134, C:S.138, C:Q.141 Salt bridges: C:R.6, C:R.134 SO4.29: 5 residues within 4Å: Chain B: R.21 Chain C: N.118, V.148, T.149, S.150 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Salt bridges: B:R.21 Hydrogen bonds: C:T.149, C:S.150, C:S.150 SO4.36: 8 residues within 4Å: Ligands: BTN-3V3-NLB-OMT-OIC-3V2.1, BTN-3V3-NLB-OMT-OIC-3V2.1, SO4.12, BTN-3V3-NLB-OMT-OIC-3V2.13, BTN-3V3-NLB-OMT-OIC-3V2.13, SO4.24, BTN-3V3-NLB-OMT-OIC-3V2.25, BTN-3V3-NLB-OMT-OIC-3V2.25 No protein-ligand interaction detected (PLIP)

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

EDO.6: 4 residues within 4Å: Chain A: E.77, N.78, G.79, Y.80 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: R.153, R.154, S.155 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: R.62, R.63 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: N.101, A.102 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: R.6, A.7, P.9, H.58, V.139 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: Q.112, N.211 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: E.77, N.78, G.79, Y.80 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: R.153, R.154, S.155 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain B: R.62, R.63 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain B: N.101, A.102 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: R.6, A.7, P.9, H.58, V.139 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain B: Q.112, N.211 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain C: E.77, N.78, G.79, Y.80 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain C: R.153, R.154, S.155 Ligand excluded by PLIP EDO.32: 2 residues within 4Å: Chain C: R.62, R.63 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain C: N.101, A.102 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain C: R.6, A.7, P.9, H.58, V.139 Ligand excluded by PLIP EDO.35: 2 residues within 4Å: Chain C: Q.112, N.211 Ligand excluded by PLIP

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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
E

C
E

Neutrophil elastase

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