1T1F

Crystal Structure of Native Antithrombin in its Monomeric Form

PDB DOI: https://doi.org/10.2210/pdb1T1F/pdb

Classification: BLOOD CLOTTING
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): Yes

Deposited: 2004-04-16 Released: 2005-10-04
Deposition Author(s): Johnson, D.J.D., Huntington, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.239
R-Value Work: 0.225

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 154.52 kDa
Atom Count: 10,296
Modelled Residue Count: 1,257
Deposited Residue Count: 1,296
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antithrombin-III	A, B, C	432	Homo sapiens	Mutation(s): 3 Gene Names: SERPINC1
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 Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F, G, I, J D, F, G, I, J, L	2		N-Glycosylation	Interactions Focus chain D Focus chain F Focus chain G Focus chain I Focus chain J Focus chain L Interactions & Density Focus chain D Focus chain F Focus chain G Focus chain I Focus chain J Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, H, K	3		N-Glycosylation	Interactions Focus chain E Focus chain H Focus chain K Interactions & Density Focus chain E Focus chain H Focus chain K
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] CA [auth C] DA [auth C] EA [auth C] FA [auth C] AA [auth B], CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain JA [auth C] SDF format, chain T [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain T [auth A]	BA [auth B], JA [auth C], T [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain JA [auth C] Focus chain T [auth A] Interactions & Density Focus chain BA [auth B] Focus chain JA [auth C] Focus chain T [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.239
R-Value Work: 0.225
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.83	α = 90
b = 43.71	β = 120.01
c = 153.93	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-10-04

Deposition Author(s):

Johnson, D.J.D.

Huntington, J.A.

Revision History (Full details and data files)

Version 1.0: 2005-10-04
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2021-10-27
Changes: Database references, Structure summary
Version 2.2: 2023-08-23
Changes: Data collection, Refinement description