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SMTL ID : 6dzf.1

Orthorhombic trypsin cryocooled to 100 K with 20% xylose as cryoprotectant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1:

8 residues within 4Å:

Chain A: E.52, D.53, N.54, I.55, V.57, V.58, E.59, E.62

5 PLIP interactions:

3 interactions with chain A, 2 Ligand-Water interactions

Metal complexes: A:E.52, A:N.54, A:V.57, H₂O.2, H₂O.2

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.2:

15 residues within 4Å:

Chain A: D.171, S.172, C.173, Q.174, S.177, V.191, W.193, G.194, S.195, G.196, C.197, A.198, P.203, G.204
Ligands: SO4.3

6 PLIP interactions:

6 interactions with chain A

Hydrophobic interactions: A:V.191
Hydrogen bonds: A:S.172, A:S.172, A:S.172, A:G.196
Water bridges: A:W.193

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

SO4.3:

5 residues within 4Å:

Chain A: H.40, Q.174, G.175, S.177
Ligands: BEN.2

3 PLIP interactions:

3 interactions with chain A

Hydrogen bonds: A:G.175, A:S.177
Salt bridges: A:H.40

1 x XYS: alpha-D-xylopyranose(Non-covalent)

XYS.4:

3 residues within 4Å:

Chain A: N.79, T.80, Q.155

1 PLIP interactions:

1 interactions with chain A

Water bridges: A:N.79

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Juers, D.H. et al., The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order. Acta Crystallogr D Struct Biol (2018)

Release Date

2018-09-19

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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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
Medium
High
Extreme

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