1R1L | pdb_00001r1l

Structure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an exogenous tripeptide (formyl-norleucine-LF)

PDB DOI: https://doi.org/10.2210/pdb1R1L/pdb

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

Deposited: 2003-09-24 Released: 2004-10-05
Deposition Author(s): Zhou, A., Huntington, J.A., Lomas, D.A., Stein, P.E., Carrell, R.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.249 (Depositor), 0.245 (DCC)
R-Value Work:
0.204 (Depositor), 0.196 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Serpins and the design of peptides to block intermolecular beta-linkages

Zhou, A., Huntington, J.A., Lomas, D.A., Stein, P.E., Carrell, R.W.

To be published.

Macromolecule Content

Total Structure Weight: 100.82 kDa
Atom Count: 6,898
Modeled Residue Count: 835
Deposited Residue Count: 874
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antithrombin-III	A [auth L], B [auth I]	432	Homo sapiens	Mutation(s): 0
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01008
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antithrombin P14-P9 peptide	C	7	N/A	Mutation(s): 0

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
EXOGENOUS TRIPEPTIDE formyl-(NLE)LF	D	3	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth L] SDF format, chain F [auth L] SDF format, chain G [auth I] SDF format, chain H [auth I] SDF format, chain I SDF format, chain J [auth I] SDF format, chain K [auth I] MOL2 format, chain E [auth L] MOL2 format, chain F [auth L] MOL2 format, chain G [auth I] MOL2 format, chain H [auth I] MOL2 format, chain I MOL2 format, chain J [auth I] MOL2 format, chain K [auth I] mmCIF format, chain E [auth L] mmCIF format, chain F [auth L] mmCIF format, chain G [auth I] mmCIF format, chain H [auth I] mmCIF format, chain I mmCIF format, chain J [auth I] mmCIF format, chain K [auth I]	E [auth L] F [auth L] G [auth I] H [auth I] I E [auth L], F [auth L], G [auth I], H [auth I], I, J [auth I], K [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth I] Focus chain H [auth I] Focus chain I Focus chain J [auth I] Focus chain K [auth I] Interactions & Density Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth I] Focus chain H [auth I] Focus chain I Focus chain J [auth I] Focus chain K [auth I]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
FOR Query on FOR Download:Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	FORMYL GROUP C H₂ O WSFSSNUMVMOOMR-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NLE Query on NLE	D	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.249 (Depositor), 0.245 (DCC)
R-Value Work: 0.204 (Depositor), 0.196 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.171	α = 90
b = 100.421	β = 104.29
c = 87.198	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
TRUNCATE	data reduction
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2004-10-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-10-05
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.5: 2023-11-15
Changes: Data collection