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SMTL ID : 5mnh.1

Cationic trypsin in complex with benzamidine (deuterated sample at 295 K)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.93 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1:

7 residues within 4Å:

Chain A: E.52, N.54, I.55, V.57, V.58, E.59, E.62

6 PLIP interactions:

4 interactions with chain A, 2 Ligand-Water interactions

Metal complexes: A:E.52, A:N.54, A:V.57, A:E.62, H₂O.1, H₂O.3

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2:	5 residues within 4Å: Chain A: H.40, Q.174, G.175, S.177 Ligands: BEN.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.175, A:S.177, A:S.177 Salt bridges: A:H.40
SO4.3:	2 residues within 4Å: Chain A: S.127, G.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.128

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.4:

14 residues within 4Å:

Chain A: D.171, S.172, C.173, Q.174, S.177, V.191, W.193, G.194, G.196, C.197, G.204, V.205, Y.206
Ligands: SO4.2

5 PLIP interactions:

5 interactions with chain A

Hydrophobic interactions: A:V.191
Hydrogen bonds: A:D.171, A:S.172, A:G.196
Water bridges: A:V.205

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Schiebel, J. et al., Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes. Nat Commun (2018)

Release Date

2018-01-17

Peptides

Cationic trypsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Cationic trypsin

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