4Y7A | pdb_00004y7a

Factor Xa complex with GTC000422

PDB DOI: https://doi.org/10.2210/pdb4Y7A/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2015-02-13 Released: 2015-09-30
Deposition Author(s): Convery, M.A., Young, R.J., Senger, S., Hamblin, J.N., Chan, C., Toomey, J.R., Watson, N.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.236 (Depositor), 0.238 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Factor Xa complex with GTC000422

Convery, M.A., Young, R.J., Senger, S., Hamblin, J.N., Chan, C., Toomey, J.R., Watson, N.S.

To be published.

Macromolecule Content

Total Structure Weight: 44.3 kDa
Atom Count: 2,515
Modeled Residue Count: 287
Deposited Residue Count: 388
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X	A	254	Homo sapiens	Mutation(s): 0 EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742 Go to UniProtKB: P00742
PHAROS: P00742 GTEx: ENSG00000126218
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X	B	134	Homo sapiens	Mutation(s): 0 EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742 Go to UniProtKB: P00742
PHAROS: P00742 GTEx: ENSG00000126218
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
987 Query on 987 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	N-[(3S)-1-{(2S)-1-[(3S)-3-aminopiperidin-1-yl]-1-oxopropan-2-yl}-2-oxopyrrolidin-3-yl]-6-chloronaphthalene-2-sulfonamid e C₂₂ H₂₇ Cl N₄ O₄ S SWAVCKCAPZVXAE-DCPHZVHLSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.236 (Depositor), 0.238 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.16	α = 90
b = 73.477	β = 90
c = 80.377	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-09-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-09-30
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 1.2: 2024-10-09
Changes: Structure summary