5MNP

Cationic trypsin in complex with N-amidinopiperidine (at 295 K)

PDB DOI: https://doi.org/10.2210/pdb5MNP/pdb

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

Deposited: 2016-12-13 Released: 2018-01-17
Deposition Author(s): Schiebel, J., Heine, A., Klebe, G.
Funding Organization(s): European Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.01 Å
R-Value Free: 0.102
R-Value Work: 0.089
R-Value Observed: 0.090

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Cationic trypsin in complex with N-amidinopiperidine (at 295 K)

Schiebel, J., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 23.78 kDa
Atom Count: 2,046
Modelled Residue Count: 223
Deposited Residue Count: 223
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	223	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRZ Query on MRZ Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	piperidine-1-carboximidamide C₆ H₁₃ N₃ QUUYRYYUKNNNNS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [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: 1.01 Å
R-Value Free: 0.102
R-Value Work: 0.089
R-Value Observed: 0.090
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.921	α = 90
b = 58.623	β = 90
c = 67.731	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2018-01-17

Deposition Author(s):

Schiebel, J.

Heine, A.

Klebe, G.

Funding Organization	Location	Grant Number
European Research Council		268145-DrugProfilBind

Revision History (Full details and data files)

Version 1.0: 2018-01-17
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

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Help and Resources

5MNP

Cationic trypsin in complex with N-amidinopiperidine (at 295 K)

Cationic trypsin in complex with N-amidinopiperidine (at 295 K)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)