6YDY

Cationic Trypsin in Complex with a D-Phe-Pro-benzylamine derivative

PDB DOI: https://doi.org/10.2210/pdb6YDY/pdb

Classification: HYDROLASE
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2020-03-21 Released: 2021-03-31
Deposition Author(s): Ngo, K., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.185
R-Value Work: 0.158
R-Value Observed: 0.160

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Cationic Trypsin in Complex with a D-Phe-Pro-benzylamine derivative

Sandner, A., Ngo, K., Schiebel, J., Marca, A., Schmidt, L., Steinmetzer, T., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 26.23 kDa
Atom Count: 1,887
Modelled Residue Count: 223
Deposited Residue Count: 246
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cationic Trypsin	A	246	Bos taurus	Mutation(s): 0 EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760 Go to UniProtKB: P00760
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K73 (Subject of Investigation/LOI) Query on K73 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2~{S})-~{N}-[[4-(aminomethyl)phenyl]methyl]-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]pyrrolidine-2-carboxamide C₂₂ H₂₈ N₄ O₂ MTUGEKUGFKKRIV-UXHICEINSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.185
R-Value Work: 0.158
R-Value Observed: 0.160
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.6	α = 90
b = 54.6	β = 90
c = 108.536	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-03-31

Deposition Author(s):

Ngo, K.

Heine, A.

Klebe, G.

Revision History (Full details and data files)

Version 1.0: 2021-03-31
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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Help and Resources

6YDY

Cationic Trypsin in Complex with a D-Phe-Pro-benzylamine derivative

Cationic Trypsin in Complex with a D-Phe-Pro-benzylamine derivative

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)