SMTL ID : 9pda.1 (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

1 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:Q.182, A:V.199 Hydrogen bonds: A:D.179, A:S.180, A:G.204 Water bridges: A:V.213

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

PG5.2: 9 residues within 4Å: Chain A: N.27, S.30, H.31, I.63, D.64, Y.139, P.140, S.141 Ligands: PG4.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.31 Water bridges: A:S.30 PG5.4: 8 residues within 4Å: Chain A: S.28, S.30, H.31, F.32, K.51, Y.139, G.183 Ligands: PG5.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.28, A:S.30, A:K.51 PG5.5: 6 residues within 4Å: Chain A: S.28, Y.50, K.51, S.52 Ligands: PG5.4, PG4.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.51, A:S.52, A:S.52 Water bridges: A:R.53

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

PG6.3: 7 residues within 4Å: Chain A: A.120, S.152, D.153, S.154, S.155, K.157, S.158 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.152, A:D.153 Water bridges: A:A.120, A:S.152, A:S.154, A:S.154, A:S.158

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

PEG.6: 5 residues within 4Å: Chain A: N.27, S.28, G.29, Q.55, R.57 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.29, A:R.57, A:R.57 Water bridges: A:N.27 PEG.7: 4 residues within 4Å: Chain A: G.11, G.12, Y.13, T.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.12 PEG.8: 6 residues within 4Å: Chain A: N.87, T.88, L.89, Q.163, W.201, G.202 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.202 PEG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.12: 2 residues within 4Å: Chain A: N.192, G.193 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.193, A:G.193 PEG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.19: 4 residues within 4Å: Chain A: V.65, L.66, E.67, G.68 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.10: 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.2, H2O.6

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

MLI.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PG4.15: 1 residues within 4Å: Chain A: S.40 No protein-ligand interaction detected (PLIP) PG4.16: 2 residues within 4Å: Chain A: Q.41, P.101 No protein-ligand interaction detected (PLIP) PG4.17: 6 residues within 4Å: Chain A: N.62, Y.139, P.140, S.141, L.142 Ligands: PG5.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.141, A:L.142 Water bridges: A:N.62 PG4.18: 8 residues within 4Å: Chain A: A.47, H.48, C.49, Y.50, K.51, T.80, F.84 Ligands: PG5.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.50, A:T.80, A:T.80

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
A

Trypsin

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