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SMTL ID : 6b6n.1

Orthorhombic trypsin (295 K) in the presence of 50% mpd

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.3

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

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

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.4:	7 residues within 4Å: Chain A: Y.5, C.7, T.11, V.12, L.117, C.137, K.139 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.139
MRD.5:	12 residues within 4Å: Chain A: C.109, A.110, S.111, A.112, I.142, L.143, S.144, D.145, M.160, F.161, Q.188, K.208 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.142, A:I.142, A:F.161 Hydrogen bonds: A:A.110 Water bridges: A:A.112

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

2017-11-01

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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