SMTL ID : 9qfv.1

Human Tryptase beta-2 (hTPSB2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-tetramer

Ligands

4 x ACT: ACETATE ION

ACT.1: 6 residues within 4Å: Chain A: L.65, Y.66, W.130, R.138, L.139, F.143 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.143 Hydrogen bonds: A:W.130 Water bridges: A:L.139 ACT.11: 5 residues within 4Å: Chain B: L.65, Y.66, W.130, L.139, F.143 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.143 Hydrogen bonds: B:Y.66 ACT.21: 4 residues within 4Å: Chain C: L.65, Y.66, W.130, L.139 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.66, C:W.130 Water bridges: C:L.139 ACT.27: 5 residues within 4Å: Chain D: L.65, Y.66, W.130, L.139, F.143 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.143 Water bridges: D:L.139

13 x EDO: 1,2-ETHANEDIOL

EDO.2: 5 residues within 4Å: Chain A: K.11, W.126, Q.147, W.206 Ligands: SO4.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.147 EDO.4: 3 residues within 4Å: Chain A: V.20, F.28, C.45 No protein-ligand interaction detected (PLIP) EDO.7: 1 residues within 4Å: Chain A: Y.232 No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain A: N.135, C.190, Q.191, G.217, C.218 Ligands: MES.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.135, A:Q.191 EDO.9: 3 residues within 4Å: Chain A: N.184, R.186, R.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.184 Water bridges: A:R.187 EDO.12: 6 residues within 4Å: Chain B: S.10, K.11, W.12, P.13, W.14, W.206 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.12 Water bridges: B:W.206 EDO.16: 6 residues within 4Å: Chain B: Q.5, W.126, Q.147, V.148, K.149, R.187 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.5, B:Q.147, B:K.149, B:K.149, B:R.187 EDO.18: 5 residues within 4Å: Chain B: K.11, W.126, Q.147, W.206 Ligands: SO4.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.147 EDO.24: 4 residues within 4Å: Chain C: W.126, Q.147, W.206 Ligands: SO4.22 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.147 EDO.26: 3 residues within 4Å: Chain C: N.184, R.186, R.187 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.184, C:R.187 EDO.28: 6 residues within 4Å: Chain D: Q.5, W.126, Q.147, V.148, K.149, R.187 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.5, D:Q.5, D:Q.147, D:K.149, D:R.187 Water bridges: D:R.187 EDO.31: 4 residues within 4Å: Chain D: W.126, Q.147, W.206 Ligands: SO4.30 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.147 Water bridges: D:W.206 EDO.34: 7 residues within 4Å: Chain D: S.10, K.11, W.12, P.13, W.14, W.206 Ligands: SO4.30 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.12 Water bridges: D:W.206

8 x SO4: SULFATE ION

SO4.3: 4 residues within 4Å: Chain A: K.11, K.201, W.206 Ligands: EDO.2 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.201, A:K.201 Salt bridges: A:K.11, A:K.201 SO4.10: 2 residues within 4Å: Chain A: Q.5, E.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.6 Water bridges: A:Q.5 SO4.14: 3 residues within 4Å: Chain B: N.184, R.186, R.187 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.184 Salt bridges: B:R.186, B:R.187 SO4.15: 4 residues within 4Å: Chain B: K.11, K.201, W.206 Ligands: EDO.18 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.11, B:W.206 Salt bridges: B:K.11, B:K.201 SO4.22: 4 residues within 4Å: Chain C: K.11, K.201, W.206 Ligands: EDO.24 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.206 Salt bridges: C:K.11, C:K.201 SO4.25: 3 residues within 4Å: Chain C: Q.5, E.6, K.146 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.6 Salt bridges: C:K.146 SO4.29: 3 residues within 4Å: Chain D: N.184, R.186, R.187 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.184 Salt bridges: D:R.186, D:R.187 SO4.30: 5 residues within 4Å: Chain D: K.11, K.201, W.206 Ligands: EDO.31, EDO.34 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:W.206 Salt bridges: D:K.11, D:K.201

4 x GOL: GLYCEROL

GOL.5: 6 residues within 4Å: Chain A: R.9, E.62, Q.63, H.64, Q.68 Chain B: Y.67 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.9, A:R.9, A:Q.63, A:H.64, A:H.64, B:Y.67 Water bridges: A:R.61, A:H.106 GOL.19: 6 residues within 4Å: Chain B: R.9, E.62, Q.63, H.64, Y.67, Q.68 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.9, B:R.9, B:Q.63, B:H.64, B:H.64 GOL.23: 6 residues within 4Å: Chain C: R.9, E.62, Q.63, H.64, Q.68 Chain D: Y.67 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.9, C:R.9, C:Q.63, C:H.64, C:H.64, C:Q.68 GOL.35: 6 residues within 4Å: Chain D: R.9, E.62, Q.63, H.64, Y.67, Q.68 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.9, D:R.9, D:E.62, D:Q.63, D:H.64, D:H.64, D:Q.68

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID

MES.6: 10 residues within 4Å: Chain A: H.44, C.190, Q.191, G.192, S.194, V.212, S.213, W.214, G.215 Ligands: EDO.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.191, A:G.192, A:S.194, A:S.194 Water bridges: A:G.215, A:G.215 Salt bridges: A:H.44 MES.17: 8 residues within 4Å: Chain B: H.44, C.190, Q.191, G.192, S.194, V.212, S.213, W.214 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.192, B:S.194, B:S.194 Water bridges: B:S.213, B:G.215 Salt bridges: B:H.44 MES.20: 8 residues within 4Å: Chain C: H.44, C.190, Q.191, G.192, S.194, V.212, S.213, W.214 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.192, C:S.194, C:S.194, C:S.194 Water bridges: C:Q.191, C:S.213, C:G.215 Salt bridges: C:H.44 MES.33: 9 residues within 4Å: Chain D: H.44, S.189, C.190, Q.191, G.192, S.194, V.212, S.213, W.214 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.192, D:S.194, D:S.194 Water bridges: D:S.213, D:G.215 Salt bridges: D:H.44

2 x 1PE: PENTAETHYLENE GLYCOL

1PE.13: 7 residues within 4Å: Chain B: V.20, F.28, C.45, V.50, K.51, D.52, A.55 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.52 1PE.32: 7 residues within 4Å: Chain D: V.20, F.28, C.45, V.50, K.51, D.52, A.55 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Porta, A. et al., Integrating Surface Plasmon Resonance and Docking Analysis for Mechanistic Insights of Tryptase Inhibitors. Molecules (2025)

Release Date

2025-03-26

Peptides

Tryptase beta-2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Tryptase beta-2

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