1PPB | pdb_00001ppb

THE REFINED 1.9 ANGSTROMS CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN: INTERACTION WITH D-PHE-PRO-ARG CHLOROMETHYLKETONE AND SIGNIFICANCE OF THE TYR-PRO-PRO-TRP INSERTION SEGMENT

PDB DOI: https://doi.org/10.2210/pdb1PPB/pdb

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

Deposited: 1991-10-24 Released: 1994-01-31
Deposition Author(s): Bode, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Work:
0.156 (Depositor)
R-Value Observed:
0.156 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment.

Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S.R., Hofsteenge, J.

(1989) EMBO J 8: 3467-3475

PubMed: 2583108 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/j.1460-2075.1989.tb08511.x
Primary Citation Related Structures:
1PPB

PubMed Abstract:
A stoichiometric complex formed between human alpha-thrombin and D-Phe-Pro-Arg chloromethylketone was crystallized in an orthorhombic crystal form. Orientation and position of a starting model derived from homologous modelling were determined by Patterson search methods. The thrombin model was completed in a cyclic modelling-crystallographic refinement procedure to a final R-value of 0.171 for X-ray data to 1.92 A. The structure is in full agreement with published cDNA sequence data. The A-chain, ordered only in its central part, is positioned along the molecular surface opposite to the active site. The B-chain exhibits the characteristic polypeptide fold of trypsin-like proteinases. Several extended insertions form, however, large protuberances; most important for interaction with macromolecular substrates is the characteristic thrombin loop around Tyr60A-Pro60B-Pro60C-Trp60D (chymotrypsinogen numbering) and the enlarged loop around the unique Trp148. The former considerably restricts the active site cleft and seems likely to be responsible for poor binding of most natural proteinase inhibitors to thrombin. The exceptional specificity of D-Phe-Pro-Arg chloromethylketone can be explained by a hydrophobic cage formed by Ile174, Trp215, Leu99, His57, Tyr60A and Trp60D. The narrow active site cleft, with a more polar base and hydrophobic rims, extends towards the arginine-rich surface of loop Lys70-Glu80 that probably represents part of the anionic binding region for hirudin and fibrinogen.

Organizational Affiliation

Max-Planck-Institut für Biochemie, Martinsried, FRG.

Macromolecule Content

Total Structure Weight: 34.33 kDa
Atom Count: 2,819
Modeled Residue Count: 295
Deposited Residue Count: 295
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-THROMBIN (SMALL SUBUNIT)	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 (LARGE SUBUNIT)	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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0G6 Query on 0G6 Download:Ideal Coordinates CCD File SDF format, chain C [auth H] MOL2 format, chain C [auth H] mmCIF format, chain C [auth H]	C [auth H]	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide C₂₁ H₃₄ Cl N₆ O₃ DVFLYEYCMMLBTQ-VSZNYVQBSA-O		Interactions Focus chain C [auth H]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000020 (0G6) Query on PRD_000020	C [auth H]	D-Phe-Pro-Arg-CH2Cl	Peptide-like / Inhibitor		Interactions Focus chain C [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Work: 0.156 (Depositor)
R-Value Observed: 0.156 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.74	α = 90
b = 67.81	β = 90
c = 61.07	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 1994-01-31

Deposition Author(s):

Bode, W.

Revision History (Full details and data files)

Version 1.0: 1994-01-31
Type: Initial release
Version 1.1: 2008-03-07
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: 2013-02-27
Changes: Other
Version 1.4: 2024-06-05
Changes: Data collection, Database references, Derived calculations, Other
Version 1.5: 2024-11-20
Changes: Structure summary