SMTL ID : 9pda.3 (3 other biounits)

Structure of Porcine Trypsin Crystals Grown From PEG and Complexed With Crystallization Additives IV

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.18 Å

Oligo State

monomer

Ligands

3 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.1: 16 residues within 4Å: Chain A: D.179, S.180, C.181, Q.182, S.185, V.199, S.200, W.201, G.202, G.204, C.205, A.206, G.212, V.213, Y.214 Ligands: PEG.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.182, A:V.199 Hydrogen bonds: A:D.179, A:S.180, A:G.204 Water bridges: A:A.206, A:V.213 BEN.2: 4 residues within 4Å: Chain A: L.66, E.70, Q.71, F.72 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.72 Hydrogen bonds: A:E.70 Water bridges: A:F.72 BEN.7: 1 residues within 4Å: Chain A: S.137 No protein-ligand interaction detected (PLIP)

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 6 residues within 4Å: Chain A: D.153, K.157, I.164, T.165, G.166 Ligands: PEG.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.157, A:G.166 Salt bridges: A:D.153

15 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 7 residues within 4Å: Chain A: N.87, T.88, L.89, W.201, G.202 Ligands: BEN.1, PEG.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.88, A:G.202, A:G.202 PEG.8: 8 residues within 4Å: Chain A: K.157, S.158, Y.160, P.161, G.162, Q.163, I.164 Ligands: EPE.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.157, A:G.162, A:Q.163, A:I.164 PEG.9: 7 residues within 4Å: Chain A: S.152, D.153, S.154 Ligands: PG5.6, PEG.16, PEG.17, PG4.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.154 PEG.10: 4 residues within 4Å: Chain A: S.28, Y.50, K.51, S.52 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.28, A:K.51, A:S.52, A:S.52 PEG.11: 4 residues within 4Å: Chain A: V.190, C.191, N.192, G.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.193 Water bridges: A:N.192 PEG.12: 7 residues within 4Å: Chain A: N.27, G.29, S.30, H.31, I.63, D.64 Ligands: PG4.25 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.27, A:G.29, A:H.31 Water bridges: A:R.57 PEG.13: 6 residues within 4Å: Chain A: Q.41, K.97, L.98, S.99, S.100, P.101 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.41, A:K.97 PEG.16: 7 residues within 4Å: Chain A: S.152, S.154, S.155, S.158 Ligands: PG5.6, PEG.9, PEG.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.154 Water bridges: A:S.158 PEG.17: 3 residues within 4Å: Chain A: S.154 Ligands: PEG.9, PEG.16 No protein-ligand interaction detected (PLIP) PEG.18: 1 residues within 4Å: Ligands: PG4.23 No protein-ligand interaction detected (PLIP) PEG.19: 2 residues within 4Å: Chain A: N.83, N.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.83 Water bridges: A:N.85 PEG.20: 7 residues within 4Å: Chain A: S.159, Y.160, P.161, G.162, Q.163, K.210 Ligands: PEG.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.210 PEG.21: 3 residues within 4Å: Chain A: P.161, G.162 Ligands: PEG.20 No protein-ligand interaction detected (PLIP) PEG.27: 1 residues within 4Å: Ligands: PG4.26 No protein-ligand interaction detected (PLIP) PEG.28: 4 residues within 4Å: Chain A: N.87, T.88, Q.163 Ligands: PEG.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.163

2 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)

PG5.5: 8 residues within 4Å: Chain A: F.32, C.33, H.48, C.49, K.51, Y.139, Q.182 Ligands: PG4.25 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.182, A:Q.182 PG5.6: 8 residues within 4Å: Chain A: A.120, S.152, D.153, S.154, K.216 Ligands: PEG.9, PEG.16, PG4.22 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.153 Water bridges: A:A.120, A:A.120, A:A.120, A:S.152, A:K.216

1 x CA: CALCIUM ION(Non-covalent)

CA.14: 8 residues within 4Å: Chain A: E.60, H.61, N.62, I.63, V.65, L.66, E.67, E.70 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.60, A:N.62, A:V.65, A:E.70, H2O.3, H2O.5

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.15: 1 residues within 4Å: Chain A: R.115 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.115 Salt bridges: A:R.115

5 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.22: 3 residues within 4Å: Ligands: PG5.6, PEG.9, PG4.23 No protein-ligand interaction detected (PLIP) PG4.23: 2 residues within 4Å: Ligands: PEG.18, PG4.22 No protein-ligand interaction detected (PLIP) PG4.24: 8 residues within 4Å: Chain A: T.14, T.132, S.138, Y.139, P.140, S.141, L.142, Q.144 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.141, A:L.142 Water bridges: A:G.12, A:S.138, A:Q.144 PG4.25: 9 residues within 4Å: Chain A: S.30, H.31, I.63, D.64, Y.139, P.140, S.141 Ligands: PG5.5, PEG.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.30, A:Y.139 Water bridges: A:S.30, A:Y.139, A:Y.139 PG4.26: 1 residues within 4Å: Ligands: PEG.27 No protein-ligand interaction detected (PLIP)

Links

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Citation

McPherson, A., Structure of Porcine Trypsin Crystals Grown From PEG and Complexed With Crystallization Additives IV. To Be Published

Release Date

2025-09-24

Peptides

Trypsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Trypsin

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