3KCG
Crystal structure of the antithrombin-factor IXa-pentasaccharide complex
- PDB DOI: https://doi.org/10.2210/pdb3KCG/pdb
- Classification: HYDROLASE, HYDROLASE INHIBITOR
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2009-10-21 Released: 2010-02-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.230
- R-Value Work: 0.208
- R-Value Observed: 0.208
wwPDB Validation 3D Report Full Report
This is version 2.2 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Coagulation factor IXa light chain | A [auth L] | 59 | Homo sapiens | Mutation(s): 0 Gene Names: F9 EC: 3.4.21.22 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00740 (Homo sapiens) Explore P00740 Go to UniProtKB: P00740 | |||||
PHAROS: P00740 GTEx: ENSG00000101981 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00740 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Coagulation factor IXa heavy chain | B [auth H] | 235 | Homo sapiens | Mutation(s): 1 Gene Names: F9 EC: 3.4.21.22 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00740 (Homo sapiens) Explore P00740 Go to UniProtKB: P00740 | |||||
PHAROS: P00740 GTEx: ENSG00000101981 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00740 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Antithrombin-III | C [auth I] | 432 | Homo sapiens | Mutation(s): 1 Gene Names: SERPINC1, AT3, PRO0309 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01008 (Homo sapiens) Explore P01008 Go to UniProtKB: P01008 | |||||
PHAROS: P01008 GTEx: ENSG00000117601 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01008 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | D [auth A], F [auth C] | 2 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC | |||||
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E [auth B] | 3 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO | |||||
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 3,4-di-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranose-(1-4)-2,3-di-O-methyl-beta-D-glucopyranuronic acid-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-3-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2,3,6-tri-O-sulfo-alpha-D-glucopyranoside | G [auth D] | 5 |  | N/A | |
Glycosylation Resources | |||||
GlyTouCan: G76630SM GlyCosmos: G76630SM | |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MPD Query on MPD | I, J [auth I] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| CA Query on CA | H | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900031 Query on PRD_900031 | G [auth D] | heparin pentasaccharide | Oligosaccharide / Anticoagulant |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.230
- R-Value Work: 0.208
- R-Value Observed: 0.208
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 78.78 | α = 90 |
| b = 88.44 | β = 90 |
| c = 147.23 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHASER | phasing |
| CNS | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
Entry History
Deposition Data
- Released Date: 2010-02-02 Deposition Author(s): Huntington, J.A., Johnson, D.J.D.
Revision History (Full details and data files)
- Version 1.0: 2010-02-02
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2021-11-10
Changes: Database references, Structure summary - Version 2.2: 2023-11-01
Changes: Data collection, Refinement description
