GeezerVison is showing www.rcsb.org — RCSB PDB - 1IQL: Human coagulation factor Xa in complex with M54476

1IQL | pdb_00001iql

Human coagulation factor Xa in complex with M54476

PDB DOI: https://doi.org/10.2210/pdb1IQL/pdb

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

Deposited: 2001-07-23 Released: 2003-09-23
Deposition Author(s): Shiromizu, I., Matsusue, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.304 (Depositor)
R-Value Work:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Download Mendeley

Factor Xa Specific Inhibitor that Induces the Novel Binding Model in Complex with Human Fxa

Matsusue, T., Shiromizu, I., Okamoto, A., Nakayama, K., Nishida, H., Mukaihira, T., Miyazaki, Y., Saitou, F., Morishita, H., Ohnishi, S., Mochizuki, H.

To be published.

Asymmetric Unit

Explore in 3D: Structure | Sequence Annotations | Validation Report | Ligand Interaction (XMJ)

Biological Assembly 1

Explore in 3D: Structure | Sequence Annotations | Validation Report | Ligand Interaction (XMJ)

Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 2-mer - A1B1

Find Similar Assemblies

Biological assembly 1 assigned by authors.

Macromolecule Content

Total Structure Weight: 37.65 kDa
Atom Count: 2,272
Modeled Residue Count: 286
Deposited Residue Count: 331
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
coagulation Factor Xa	A	235	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
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

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
coagulation Factor Xa	B [auth L]	96	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
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XMJ Query on XMJ 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]	4-[[(1E)-2-(4-CHLOROPHENYL)ETHENYL]SULFONYL]-1-[[1-(4-PYRIDINYL)-4-PIPERIDINYL]METHYL]PIPERAZINONE C₂₃ H₂₇ Cl N₄ O₃ S QLHUDNKWOSQSMK-CXUHLZMHSA-N		Interactions Focus chain D [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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.304 (Depositor)
R-Value Work: 0.211 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.88	α = 90
b = 78.67	β = 90
c = 55.85	γ = 90

Software Package:

Software Name	Purpose
GLRF	phasing
CNX	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-09-23

Deposition Author(s):

Shiromizu, I.

Matsusue, T.

Revision History (Full details and data files)

Version 1.0: 2003-09-23
Type: Initial release
Version 1.1: 2007-11-21
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-04
Changes: Refinement description
Version 1.4: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.5: 2024-11-20
Changes: Structure summary

GeezerVison