2GDD

Human beta II tryptase with inhibitor CRA-27592

PDB DOI: https://doi.org/10.2210/pdb2GDD/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2006-03-15 Released: 2006-04-11
Deposition Author(s): Somoza, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.254
R-Value Work: 0.215
R-Value Observed: 0.219

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Human beta II tryptase with inhibitor CRA-27592

Somoza, J.R.

To be published.

Macromolecule Content

Total Structure Weight: 112.28 kDa
Atom Count: 7,984
Modelled Residue Count: 972
Deposited Residue Count: 980
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptase beta-2	A, B, C, D	245	Homo sapiens	Mutation(s): 0 Gene Names: TPSB2, TPS2 EC: 3.4.21.59
UniProt & NIH Common Fund Data Resources
Find proteins for P20231 (Homo sapiens) Explore P20231 Go to UniProtKB: P20231
PHAROS: P20231 GTEx: ENSG00000197253
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20231
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5AM Query on 5AM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	BENZYL {(1S)-5-AMINO-1-[(S)-HYDROXY(5-{[4-(4-PHENYLBUTANOYL)PIPERAZIN-1-YL]METHYL}-1,2,4-OXADIAZOL-3-YL)METHYL]PENTYL}CARBAMATE C₃₁ H₄₂ N₆ O₅ LRPAFCFDXNPFAF-WNJJXGMVSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.254
R-Value Work: 0.215
R-Value Observed: 0.219
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.015	α = 90
b = 78.015	β = 90
c = 163.98	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-04-11

Deposition Author(s):

Somoza, J.R.

Revision History (Full details and data files)

Version 1.0: 2006-04-11
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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Help and Resources

2GDD

Human beta II tryptase with inhibitor CRA-27592

Human beta II tryptase with inhibitor CRA-27592

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)