3U8O

Human thrombin complexed with D-Phe-Pro-D-Arg-D-Thr

PDB DOI: https://doi.org/10.2210/pdb3U8O/pdb

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

Deposited: 2011-10-17 Released: 2012-05-23
Deposition Author(s): Figueiredo, A.C., Clement, C.C., Philipp, M., Pereira, P.J.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free: 0.149
R-Value Work: 0.128
R-Value Observed: 0.129

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 34.46 kDa
Atom Count: 2,937
Modelled Residue Count: 286
Deposited Residue Count: 294
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A [auth L]	30	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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
D-PHE-PRO-D-ARG-D-THR DERIVED DIRECT THROMBIN INHIBITOR	C [auth I]	5	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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]	D [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain F [auth H] MOL2 format, chain F [auth H]	F [auth H]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain F [auth H] Interactions & Density Focus chain F [auth H]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain H SDF format, chain I [auth H] MOL2 format, chain H MOL2 format, chain I [auth H]	H, I [auth H]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain H Focus chain I [auth H] Interactions & Density Focus chain H Focus chain I [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth H] MOL2 format, chain G [auth H]	G [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth H] Interactions & Density Focus chain G [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth H] MOL2 format, chain E [auth H]	E [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Interactions & Density Focus chain E [auth H]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000940 Query on PRD_000940	C [auth I]	D-phenylalanyl-L-prolyl-N~5~-[amino(iminio)methyl]-D-ornithyl-D-threoninamide	Peptide-like / Thrombin inhibitor		Interactions Focus chain C [auth I] Interactions & Density Focus chain C [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free: 0.149
R-Value Work: 0.128
R-Value Observed: 0.129
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.15785/SBGRID/103
Diffraction Data: https://doi.org/10.15785/SBGRID/104
Diffraction Data: https://doi.org/10.15785/SBGRID/105

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.446	α = 90
b = 72.68	β = 90
c = 83.09	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-05-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-05-23
Type: Initial release
Version 1.1: 2013-04-17
Changes: Other
Version 1.2: 2013-06-05
Changes: Other
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

3U8O

Human thrombin complexed with D-Phe-Pro-D-Arg-D-Thr

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

Sequence Annotations

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Entity ID: 3

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)