1IOE|pdb_00001ioe
Human coagulation factor Xa in complex with M55532
- PDB DOI: https://doi.org/10.2210/pdb1IOE/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Mutation(s): No
- Deposited: 2001-03-08 Released: 2003-09-23
- Deposition Author(s): Shiromizu, I.,Matsusue, T.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.295 (Depositor)
- R-Value Work: 0.201 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.5 of the entry. See complete history.
Literature
Download MendeleyFactor 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.
Explore in 3D: Structure |Sequence Annotations |Validation Report |Ligand Interaction (XMA)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 2-mer - A1B1
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA,PQS (software)
Macromolecule Content
- Total Structure Weight: 37.74 kDa
- Atom Count: 2,278
- Modeled Residue Count: 286
- Deposited Residue Count: 331
- Unique protein chains: 2
Macromolecules
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| COAGULATION FACTOR XA | 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 | |||||
PHAROS: P00742 GTEx: ENSG00000126218 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00742 | ||||
Sequence AnnotationsExpand | |||||
| |||||
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 | |||||
PHAROS: P00742 GTEx: ENSG00000126218 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00742 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| XMA Query on XMA Download Ideal Coordinates CCD File | D [auth A] | (-)-7-[(6-CHLORO-2-NAPHTHALENYL)SULFONYL]TETRAHYDRO-8A-(METHOXYMETHYL)-1'-(4-PYRIDINYL)-SPIRO[5H-OXAZOLO[3,2-A]PYRAZINE-2(3H),4'-PIPERIDIN]-5-ONE C27 H29 Cl N4 O5 S OCCGRNQFQCNISA-MHZLTWQESA-N |  | ||
| CA Query on CA Download Ideal Coordinates CCD File | C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.295 (Depositor)
- R-Value Work: 0.201 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.7 | α = 90 |
| b = 78.17 | β = 90 |
| c = 56.04 | γ = 90 |
| Software Name | Purpose |
|---|---|
| GLRF | phasing |
| CNX | refinement |
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: Derived calculations, 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: 2024-10-23
Changes: Structure summary
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.