SMTL ID : 9pct.1

Structure of Porcine Trypsin Crystals Grown from PEG Complexed with Crystallization Additives III

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Post Translational Modification)

GLC-FRU.1: 13 residues within 4Å: Chain A: H.31, F.32, C.33, G.34, H.48, C.49, Y.139, Q.182, G.183, D.184, S.185 Ligands: BEN.4, PEG.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.48, A:Q.182, A:F.32, A:H.48, A:G.183, A:G.183, A:G.183, A:S.185

1 x FRU- GLC: alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose(Non-covalent)

FRU-GLC.2: 11 residues within 4Å: Chain A: N.87, T.88, L.89, Y.160, Q.163, M.168, W.201, G.202, Y.203, G.204 Ligands: ACT.29 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.202, A:G.202 Water bridges: A:Q.163, A:Q.163, A:Q.163, A:G.202, A:G.202

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 8 residues within 4Å: Chain A: E.60, H.61, N.62, I.63, V.65, L.66, E.67, E.70 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.60, A:N.62, A:E.67, A:E.70, H2O.1

3 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.4: 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: GLC-FRU.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.199 Hydrogen bonds: A:S.180, A:S.180, A:G.204 Water bridges: A:D.179, A:V.213 BEN.20: 1 residues within 4Å: Ligands: ACT.19 No protein-ligand interaction detected (PLIP) BEN.34: 5 residues within 4Å: Chain A: N.39, S.40, L.104, T.110 Ligands: FLC.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.104 Hydrogen bonds: A:T.110, A:T.110

2 x FLC: CITRATE ANION(Non-covalent)(Non-functional Binders)

FLC.5: 7 residues within 4Å: Chain A: L.104, N.105, S.106, V.108, A.109, T.110 Ligands: BEN.34 No protein-ligand interaction detected (PLIP) FLC.37: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PG4.6: 5 residues within 4Å: Chain A: S.152, S.154, S.155, S.158 Ligands: MLT.21 No protein-ligand interaction detected (PLIP) PG4.9: 10 residues within 4Å: Chain A: V.10, G.11, G.12, T.132, K.133, S.134, Q.144, G.177 Ligands: EPE.15, ACT.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.11, A:T.132 Water bridges: A:G.12, A:S.134

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

PEG.7: 2 residues within 4Å: Chain A: K.208 Ligands: TAR.38 No protein-ligand interaction detected (PLIP) PEG.8: 4 residues within 4Å: Chain A: F.32, K.51 Ligands: GLC-FRU.1, GLC-FRU.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.51 PEG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.24: 2 residues within 4Å: Ligands: PG5.22, PEG.26 No protein-ligand interaction detected (PLIP) PEG.25: 1 residues within 4Å: Ligands: PEG.26 No protein-ligand interaction detected (PLIP) PEG.26: 3 residues within 4Å: Ligands: PG6.14, PEG.24, PEG.25 No protein-ligand interaction detected (PLIP) PEG.27: 4 residues within 4Å: Chain A: Q.55, F.72, I.73, N.74 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.72, A:N.74 PEG.32: 1 residues within 4Å: Ligands: PG6.31 No protein-ligand interaction detected (PLIP) PEG.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: V.111, S.112, L.113, R.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.113, A:R.115, A:R.115 GOL.23: 6 residues within 4Å: Chain A: L.151, G.172, F.173, L.174, E.175, G.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.172, A:L.174, A:E.175

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

PG5.11: 4 residues within 4Å: Chain A: K.147 Ligands: MLT.13, PG6.14, PG5.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.147 PG5.22: 2 residues within 4Å: Ligands: MLT.13, PEG.24 No protein-ligand interaction detected (PLIP) PG5.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PG5.30: 7 residues within 4Å: Chain A: H.81, N.83, D.90, N.91, N.167, Y.220 Ligands: MLT.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.91, A:N.167 PG5.33: 10 residues within 4Å: Chain A: E.123, C.124, L.125, K.147, V.190, C.191, N.192, G.193 Ligands: PG5.11, PG6.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.192

3 x MLT: D-MALATE(Non-functional Binders)(Non-covalent)

MLT.13: 2 residues within 4Å: Ligands: PG5.11, PG5.22 No protein-ligand interaction detected (PLIP) MLT.21: 6 residues within 4Å: Chain A: A.119, A.120, S.152, D.153, S.154 Ligands: PG4.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.120, A:D.153 Water bridges: A:L.151, A:S.154 MLT.35: 1 residues within 4Å: Ligands: PG5.30 No protein-ligand interaction detected (PLIP)

2 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-functional Binders)(Non-covalent)

PG6.14: 4 residues within 4Å: Ligands: PG5.11, ACT.19, PEG.26, PG5.33 No protein-ligand interaction detected (PLIP) PG6.31: 2 residues within 4Å: Chain A: K.133 Ligands: PEG.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.133

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

EPE.15: 9 residues within 4Å: Chain A: T.14, T.132, K.133, S.138, P.140, S.141, L.142, Q.144 Ligands: PG4.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.141, A:L.142 Water bridges: A:Q.144, A:Q.144 EPE.16: 6 residues within 4Å: Chain A: Q.41, W.42, K.77, K.97, I.228, N.231 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.41, A:W.42, A:K.97, A:I.228 Salt bridges: A:K.77, A:K.97

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.17: 1 residues within 4Å: Ligands: PG4.9 No protein-ligand interaction detected (PLIP) ACT.19: 2 residues within 4Å: Ligands: PG6.14, BEN.20 No protein-ligand interaction detected (PLIP) ACT.29: 2 residues within 4Å: Chain A: Y.203 Ligands: FRU-GLC.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.203

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.18: 4 residues within 4Å: Chain A: N.27, G.29, S.30, R.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.27 Salt bridges: A:R.57

1 x TAR: D(-)-TARTARIC ACID(Non-functional Binders)

TAR.38: 1 residues within 4Å: Ligands: PEG.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McPherson, A., Structure of Porcine Trypsin Crystals Grown from PEG Complexed with Crystallization Additives III. To Be Published

Release Date

2025-09-17

Peptides

Trypsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Trypsin

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