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SMTL ID : 2j9n.1

Robotically harvested Trypsin complexed with Benzamidine containing polypeptide mediated crystal contacts

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLN- UNK- UNK: UNKNOWN PEPTIDE(Non-covalent)

GLN-UNK-UNK.1:

7 residues within 4Å:

Chain A: F.24, H.40, Y.42, K.43, Q.174, G.175, S.177

7 PLIP interactions:

7 interactions with chain A

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

1 x CA: CALCIUM ION(Non-covalent)

CA.2:

4 residues within 4Å:

Chain A: E.52, N.54, V.57, 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.2, H₂O.3

1 x NA: SODIUM ION(Non-functional Binders)

NA.3:

3 residues within 4Å:

Chain A: T.107, S.108, K.186

3 PLIP interactions:

3 interactions with chain A

Hydrogen bonds: A:T.107, A:S.108, A:S.108

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.4:

11 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

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 IPH: PHENOL(Non-covalent)

IPH.5:

3 residues within 4Å:

Chain A: S.130, Y.131, D.133

No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Viola, R. et al., Operator Assisted Harvesting of Protein Crystals Using a Universal Micromanipulation Robot. J.Appl.Crystallogr. (2007)

Release Date

2007-04-03

Peptides

CATIONIC TRYPSIN: A
UNKNOWN PEPTIDE: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

CATIONIC TRYPSIN

UNKNOWN PEPTIDE

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