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SMTL ID : 6avl.1

Orthorhombic Trypsin (295 K) in the presence of 50% xylose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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

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.2

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.2:

14 residues within 4Å:

Chain A: D.171, S.172, C.173, Q.174, S.177, V.191, S.192, W.193, G.194, G.196, C.197, A.198, G.204
Ligands: SO4.3

5 PLIP interactions:

5 interactions with chain A

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

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

4 PLIP interactions:

4 interactions with chain A

Hydrogen bonds: A:Q.174, A:G.175, A:S.177
Salt bridges: A:H.40

1 x XYP: beta-D-xylopyranose(Non-covalent)

XYP.4:

8 residues within 4Å:

Chain A: Q.115, C.116, L.117, K.139, V.182, C.183, S.184, G.185

5 PLIP interactions:

5 interactions with chain A

Hydrogen bonds: A:Q.115, A:Q.115, A:S.184, A:G.185
Salt bridges: A:K.139

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

XYS.5:

4 residues within 4Å:

Chain A: N.79, T.80, Q.155, W.193

3 PLIP interactions:

3 interactions with chain A

Water bridges: A:G.154, A:Q.155, A:Q.155

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

2017-09-20

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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