SMTL ID : 9pda.4 (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: 15 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.199 Hydrogen bonds: A:D.179, A:S.180, A:G.204 Water bridges: A:W.201, A:Y.203 BEN.6: 2 residues within 4Å: Chain A: Y.13, K.147 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.13 Hydrogen bonds: A:K.147 Water bridges: A:Y.13 pi-Stacking: A:Y.13 BEN.9: 8 residues within 4Å: Chain A: H.31, F.32, K.51, G.130, Y.139, Q.182, G.183 Ligands: PEG.24 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.32 Hydrogen bonds: A:Y.139, A:Y.139

1 x PMA: PYROMELLITIC ACID(Non-covalent)

PMA.2: 7 residues within 4Å: Chain A: C.218, N.219, Y.220, V.221, N.222, W.223 Ligands: PG4.33 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.222, A:W.223 Water bridges: A:C.218, A:V.221, A:N.222

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

PG5.3: 9 residues within 4Å: Chain A: S.112, L.113, P.114, R.115, Q.194, V.221, N.222, Q.225 Ligands: PG5.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.112, A:R.115, A:Q.225 PG5.4: 4 residues within 4Å: Chain A: Q.225 Ligands: PG5.3, PEG.7, PEG.36 No protein-ligand interaction detected (PLIP) PG5.12: 6 residues within 4Å: Chain A: T.88, G.162, Q.163, I.164, T.165 Ligands: PG4.32 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.164

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

EPE.5: 9 residues within 4Å: Chain A: T.14, T.132, S.138, P.140, S.141, L.142, Q.144 Ligands: PEG.18, PEG.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.141, A:L.142, A:Q.144 Water bridges: A:T.14

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

PEG.7: 3 residues within 4Å: Chain A: R.115 Ligands: PG5.4, PEG.8 Ligand excluded by PLIP PEG.8: 2 residues within 4Å: Chain A: R.115 Ligands: PEG.7 Ligand excluded by PLIP PEG.10: 4 residues within 4Å: Chain A: K.157, S.158, P.161 Ligands: PG4.32 Ligand excluded by PLIP PEG.11: 4 residues within 4Å: Chain A: N.27, R.57, L.66, F.72 Ligand excluded by PLIP PEG.16: 1 residues within 4Å: Ligands: PEG.27 Ligand excluded by PLIP PEG.17: 5 residues within 4Å: Chain A: S.40, Q.41, P.101, A.102 Ligands: PEG.35 Ligand excluded by PLIP PEG.18: 7 residues within 4Å: Chain A: H.61, N.62, V.65, E.67, S.141, L.142 Ligands: EPE.5 Ligand excluded by PLIP PEG.19: 2 residues within 4Å: Ligands: PEG.20, PEG.23 Ligand excluded by PLIP PEG.20: 8 residues within 4Å: Chain A: D.64, S.138, Y.139, P.140, S.141 Ligands: EPE.5, PEG.19, PEG.23 Ligand excluded by PLIP PEG.21: 1 residues within 4Å: Ligands: PEG.22 Ligand excluded by PLIP PEG.22: 1 residues within 4Å: Ligands: PEG.21 Ligand excluded by PLIP PEG.23: 6 residues within 4Å: Chain A: S.137, S.138, Y.139, P.140 Ligands: PEG.19, PEG.20 Ligand excluded by PLIP PEG.24: 8 residues within 4Å: Chain A: F.32, C.33, A.47, H.48, C.49, Y.50, K.51 Ligands: BEN.9 Ligand excluded by PLIP PEG.25: 5 residues within 4Å: Chain A: S.28, Y.50, K.51, S.52, R.53 Ligand excluded by PLIP PEG.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PEG.27: 1 residues within 4Å: Ligands: PEG.16 Ligand excluded by PLIP PEG.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PEG.35: 6 residues within 4Å: Chain A: N.39, S.40, Q.41, W.42, I.228 Ligands: PEG.17 Ligand excluded by PLIP PEG.36: 4 residues within 4Å: Chain A: Q.225, Q.226, A.229 Ligands: PG5.4 Ligand excluded by PLIP PEG.37: 3 residues within 4Å: Chain A: R.53, N.74 Ligands: PG4.29 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.13: 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.1, H2O.6 CA.14: 3 residues within 4Å: Chain A: L.104, A.109, T.110 No protein-ligand interaction detected (PLIP)

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

MLI.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PG4.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PG4.29: 5 residues within 4Å: Chain A: S.52, R.53, N.74, A.75 Ligands: PEG.37 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.53, A:N.74 Water bridges: A:Y.50, A:Y.50, A:I.54, A:A.75 PG4.30: 8 residues within 4Å: Chain A: N.131, K.133, S.134, S.135, G.136, C.181, G.204, C.205 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.133, A:C.205 Water bridges: A:Q.182 PG4.31: 6 residues within 4Å: Chain A: T.14, C.15, A.16, A.17, H.61, L.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.14, A:A.17 PG4.32: 2 residues within 4Å: Ligands: PEG.10, PG5.12 No protein-ligand interaction detected (PLIP) PG4.33: 6 residues within 4Å: Chain A: H.81, P.82, N.222, W.223, Q.226 Ligands: PMA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.226 Water bridges: A:N.222

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.38: 2 residues within 4Å: Chain A: N.85, N.87 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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
D

Trypsin

Related Entries With Identical Sequence