3EDX | pdb_00003edx

Crystal structure of the W215A/E217A mutant of murine thrombin

PDB DOI: https://doi.org/10.2210/pdb3EDX/pdb

Classification: HYDROLASE
Organism(s): Mus musculus
Expression System: Cricetulus griseus
Mutation(s): Yes

Deposited: 2008-09-03 Released: 2009-07-07
Deposition Author(s): Gandhi, P.S., Page, M.J., Chen, Z., Bush-pelc, L., Di Cera, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.243 (Depositor), 0.243 (DCC)
R-Value Work:
0.214 (Depositor), 0.214 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Molecular Basis for the Kinetic Differences of the W215A/E217A Mutant of Human and Murine Thrombin

Gandhi, P.S., Page, M.J., Chen, Z., Bush-Pelc, L., Di Cera, E.

To be published.

Macromolecule Content

Total Structure Weight: 106.04 kDa
Atom Count: 7,612
Modeled Residue Count: 900
Deposited Residue Count: 906
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A, C, E	44	Mus musculus	Mutation(s): 0 Gene Names: F2, Cf2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P19221 (Mus musculus) Explore P19221 Go to UniProtKB: P19221
IMPC: MGI:88380
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19221
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin heavy chain	B, D, F	258	Mus musculus	Mutation(s): 2 Gene Names: F2, Cf2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P19221 (Mus musculus) Explore P19221 Go to UniProtKB: P19221
IMPC: MGI:88380
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19221
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D Focus chain F	Go to GlyGen: P19221-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth F] SDF format, chain M [auth D] SDF format, chain I [auth B] MOL2 format, chain P [auth F] MOL2 format, chain M [auth D] MOL2 format, chain I [auth B] mmCIF format, chain P [auth F] mmCIF format, chain M [auth D] mmCIF format, chain I [auth B]	I [auth B], M [auth D], P [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth B] Focus chain M [auth D] Focus chain P [auth F] Interactions & Density Focus chain I [auth B] Focus chain M [auth D] Focus chain P [auth F]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth F] SDF format, chain N [auth F] SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain J [auth D] SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain O [auth F] MOL2 format, chain N [auth F] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain O [auth F] mmCIF format, chain N [auth F] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	G [auth B] H [auth B] J [auth D] K [auth D] L [auth D] G [auth B], H [auth B], J [auth D], K [auth D], L [auth D], N [auth F], O [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Focus chain N [auth F] Focus chain O [auth F] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Focus chain N [auth F] Focus chain O [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.243 (Depositor), 0.243 (DCC)
R-Value Work: 0.214 (Depositor), 0.214 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.716	α = 90
b = 105.76	β = 90
c = 176.811	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-07-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-07-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2021-10-20
Changes: Database references, Structure summary
Version 1.4: 2023-08-30
Changes: Data collection, Refinement description
Version 1.5: 2024-11-06
Changes: Structure summary