1A2C | pdb_00001a2c

Structure of thrombin inhibited by AERUGINOSIN298-A from a BLUE-GREEN ALGA

PDB DOI: https://doi.org/10.2210/pdb1A2C/pdb

Classification: Hydrolase/Hydrolase Inhibitor
Organism(s): Homo sapiens, Hirudo medicinalis, Microcystis aeruginosa
Mutation(s): No

Deposited: 1997-12-26 Released: 1998-07-01
Deposition Author(s): Rios-Steiner, J.L., Murakami, M., Tulinsky, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Work:
0.150 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Structure of Thrombin Inhibited by Aeruginosin 298-A from a Blue-Green Alga

Steiner, J.L.R., Murakami, M., Tulinsky, A.

(1998) J Am Chem Soc 120: 597

Macromolecule Content

Total Structure Weight: 36.04 kDa
Atom Count: 2,629
Modeled Residue Count: 302
Deposited Residue Count: 311
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	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
Thrombin heavy chain	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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin variant-2	C [auth I]	12	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P09945 (Hirudo medicinalis) Explore P09945 Go to UniProtKB: P09945
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09945
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Aeruginosin 298-A	D [auth J]	4	Microcystis aeruginosa	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth H] MOL2 format, chain E [auth H] mmCIF format, chain E [auth H]	E [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth H]

Non-standard Monomers 3 Unique
ID	Chains	Type	Formula	2D Diagram
TYS Query on TYS	C [auth I]	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S
OAR Query on OAR	D [auth J]	PEPTIDE-LIKE	C₆ H₁₆ N₄ O
PRJ Query on PRJ	D [auth J]	L-PEPTIDE LINKING	C₉ H₁₅ N O₃

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000555 Query on PRD_000555	D [auth J]	AERUGINOSIN 298-A	Oligopeptide / Thrombin inhibitor, Trypsin inhibitor		Interactions Focus chain D [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Work: 0.150 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.97	α = 90
b = 72.48	β = 100.93
c = 72.24	γ = 90

Software Package:

Software Name	Purpose
RIGAKU	data collection
RIGAKU	data reduction
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
RIGAKU	data scaling
X-PLOR	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 1998-07-01

Deposition Author(s):

Rios-Steiner, J.L.

Murakami, M.

Tulinsky, A.

Revision History (Full details and data files)

Version 1.0: 1998-07-01
Type: Initial release
Version 1.1: 2008-03-24
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: 2012-12-12
Changes: Other
Version 1.4: 2013-06-05
Changes: Atomic model
Version 1.5: 2023-08-02
Changes: Advisory, Database references, Derived calculations, Other, Refinement description
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Derived calculations