SMTL ID : 9pda.2 (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: 14 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, G.212, V.213, Y.214 5 PLIP interactions: 5 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 BEN.3: 8 residues within 4Å: Chain A: E.70, Q.71, F.72, I.73, S.100, P.101, A.102, T.103 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.71, A:Q.71 Hydrogen bonds: A:Q.71, A:S.100, A:T.103 BEN.4: 3 residues within 4Å: Chain A: Y.203, G.204, Q.207 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.203 Water bridges: A:Y.203, A:Q.207

1 x PMA: PYROMELLITIC ACID(Non-covalent)

PMA.2: 8 residues within 4Å: Chain A: C.218, N.219, Y.220, V.221, N.222, W.223 Ligands: PEG.25, PG4.30 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.222, A:W.223 Water bridges: A:N.219, A:V.221, A:V.221, A:V.221, A:N.222, A:N.222

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

PG5.5: 5 residues within 4Å: Chain A: S.40, P.101, A.102, T.103, L.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.104 Water bridges: A:T.103 PG5.7: 6 residues within 4Å: Chain A: L.113, P.114, R.115, V.221, Q.225 Ligands: PG4.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.115 PG5.11: 8 residues within 4Å: Chain A: T.14, C.15, A.16, L.142, Q.144 Ligands: PEG.16, PEG.17, MLI.21 No protein-ligand interaction detected (PLIP) PG5.27: 1 residues within 4Å: Ligands: PEG.26 No protein-ligand interaction detected (PLIP)

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

PEG.6: 6 residues within 4Å: Chain A: F.32, C.33, H.48, C.49, Y.50, K.51 Ligand excluded by PLIP PEG.8: 2 residues within 4Å: Chain A: N.222 Ligands: PG4.30 Ligand excluded by PLIP PEG.9: 8 residues within 4Å: Chain A: I.20, Y.22, T.110, V.111, S.112, L.125, V.190, G.193 Ligand excluded by PLIP PEG.10: 4 residues within 4Å: Chain A: G.11, G.12, Y.13 Ligands: PEG.17 Ligand excluded by PLIP PEG.12: 3 residues within 4Å: Chain A: I.228, A.229, N.231 Ligand excluded by PLIP PEG.13: 3 residues within 4Å: Chain A: I.38, N.39, I.228 Ligand excluded by PLIP PEG.14: 3 residues within 4Å: Chain A: L.66, E.67, G.68 Ligand excluded by PLIP PEG.15: 3 residues within 4Å: Chain A: D.64, V.65, S.141 Ligand excluded by PLIP PEG.16: 9 residues within 4Å: Chain A: Y.13, T.14, T.132, P.140, S.141, L.142, Q.144 Ligands: PG5.11, PEG.17 Ligand excluded by PLIP PEG.17: 8 residues within 4Å: Chain A: Y.13, T.14, C.15, A.16 Ligands: PEG.10, PG5.11, PEG.16, MLI.21 Ligand excluded by PLIP PEG.18: 6 residues within 4Å: Chain A: S.154, K.157, S.158, P.161, G.162 Ligands: PEG.19 Ligand excluded by PLIP PEG.19: 4 residues within 4Å: Chain A: S.158, P.161 Ligands: PEG.18, PEG.23 Ligand excluded by PLIP PEG.22: 5 residues within 4Å: Chain A: E.175, G.176, A.206, Q.207, K.208 Ligand excluded by PLIP PEG.23: 1 residues within 4Å: Ligands: PEG.19 Ligand excluded by PLIP PEG.24: 5 residues within 4Å: Chain A: N.222, Q.225, Q.226, A.229 Ligands: PG4.30 Ligand excluded by PLIP PEG.25: 6 residues within 4Å: Chain A: H.81, N.222, W.223, Q.226 Ligands: PMA.2, PG4.30 Ligand excluded by PLIP PEG.26: 2 residues within 4Å: Chain A: T.103 Ligands: PG5.27 Ligand excluded by PLIP PEG.31: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.20: 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.4

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

MLI.21: 4 residues within 4Å: Chain A: A.16, A.17 Ligands: PG5.11, PEG.17 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.17

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

PG4.28: 4 residues within 4Å: Chain A: S.154, S.155, S.158, L.174 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.154 PG4.29: 3 residues within 4Å: Chain A: R.115, S.116 Ligands: PG5.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.115, A:R.115 PG4.30: 5 residues within 4Å: Chain A: N.222 Ligands: PMA.2, PEG.8, PEG.24, PEG.25 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
B

Trypsin

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