4THN | pdb_00004thn

THE CRYSTAL STRUCTURE OF ALPHA-THROMBIN-HIRUNORM IV COMPLEX REVEALS A NOVEL SPECIFICITY SITE RECOGNITION MODE.

PDB DOI: https://doi.org/10.2210/pdb4THN/pdb

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

Deposited: 1998-09-18 Released: 1999-06-15
Deposition Author(s): Lombardi, A., De Simone, G., Nastri, F., Galdiero, S., Della Morte, R., Staiano, N., Pedone, C., Bolognesi, M., Pavone, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Work:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The crystal structure of alpha-thrombin-hirunorm IV complex reveals a novel specificity site recognition mode.

Lombardi, A., De Simone, G., Nastri, F., Galdiero, S., Della Morte, R., Staiano, N., Pedone, C., Bolognesi, M., Pavone, V.

(1999) Protein Sci 8: 91-95

PubMed: 10210187 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1110/ps.8.1.91
Primary Citation Related Structures:
4THN

PubMed Abstract:
The X-ray crystal structure of the human alpha-thrombin-hirunorm IV complex has been determined at 2.5 A resolution, and refined to an R-factor of 0.173. The structure reveals an inhibitor binding mode distinctive of a true hirudin mimetic, which justifies the high inhibitory potency and the selectivity of hirunorm IV. This novel inhibitor, composed of 26 amino acids, interacts through the N-terminal end with the alpha-thrombin active site in a nonsubstrate mode, and binds specifically to the fibrinogen recognition exosite through the C-terminal end. The backbone of the N-terminal tripeptide Chg1"-Arg2"-2Na13" (Chg, cyclohexyl-glycine; 2Na1, beta-(2-naphthyl)-alanine) forms a parallel beta-strand to the thrombin main-chain segment Ser214-Gly216. The Chg1" side chain occupies the S2 site, Arg2" penetrates into the S1 specificity site, while the 2Na13" side chain occupies the aryl binding site. The Arg2" side chain enters the S1 specificity pocket from a position quite apart from the canonical P1 site. This notwithstanding, the Arg2" side chain establishes the typical ion pair with the carboxylate group of Asp189.

Organizational Affiliation

Centro Interuniversitario di Ricerca su Peptidi Bioattivi & Centro di Studio di Biocristallografia-CNR, University of Napoli Federico II, Italy.

Macromolecule Content

Total Structure Weight: 37.11 kDa
Atom Count: 2,566
Modeled Residue Count: 303
Deposited Residue Count: 321
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-THROMBIN	A [auth L]	36	Homo sapiens	Mutation(s): 0 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734
PHAROS: P00734 GTEx: ENSG00000180210
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-THROMBIN	B [auth H]	259	Homo sapiens	Mutation(s): 0 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734
PHAROS: P00734 GTEx: ENSG00000180210
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00734
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B [auth H]	Go to GlyGen: P00734-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIRUNORM IV	C [auth I]	26	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth H]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB Query on AIB	C [auth I]	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
ALC Query on ALC	C [auth I]	L-PEPTIDE LINKING	C₉ H₁₇ N O₂		ALA
BAL Query on BAL	C [auth I]	PEPTIDE-LIKE	C₃ H₇ N O₂		--
CHG Query on CHG	C [auth I]	L-PEPTIDE LINKING	C₈ H₁₅ N O₂		--
DAL Query on DAL	C [auth I]	D-PEPTIDE LINKING	C₃ H₇ N O₂		--
DGL Query on DGL	C [auth I]	D-PEPTIDE LINKING	C₅ H₉ N O₄		--
HMF Query on HMF	C [auth I]	D-PEPTIDE LINKING	C₁₀ H₁₃ N O₂		--
NAL Query on NAL	C [auth I]	L-PEPTIDE LINKING	C₁₃ H₁₃ N O₂		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Work: 0.173 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.3	α = 90
b = 72.7	β = 100
c = 73.6	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
CCP4	data reduction
CCP4	model building
TNT	refinement
CCP4	data scaling
CCP4	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 1999-06-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1999-06-15
Type: Initial release
Version 1.1: 2008-03-25
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: 2023-08-09
Changes: Advisory, Database references, Refinement description, Structure summary