3U98

Human Thrombin In Complex With MI001

PDB DOI: https://doi.org/10.2210/pdb3U98/pdb

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

Deposited: 2011-10-18 Released: 2012-10-24
Deposition Author(s): Biela, A., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.187
R-Value Work: 0.164
R-Value Observed: 0.165

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

Thrombin Inhibition

Biela, A., Sielaff, F., Heine, A., Steinmetzer, T., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 36.46 kDa
Atom Count: 2,771
Modelled Residue Count: 290
Deposited Residue Count: 308
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]	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% 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
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B [auth H]	Go to GlyGen: P00734-1
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]	13	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P09945 (Hirudo medicinalis) Explore P09945 Go to UniProtKB: P09945
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09945
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BJA Query on BJA 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]	(2S)-1-[(2R)-2-(benzylsulfonylamino)-5-guanidino-pentanoyl]-N-[(4-carbamimidoylphenyl)methyl]pyrrolidine-2-carboxamide C₂₆ H₃₆ N₈ O₄ S QKFCYPKTTJCUSZ-YADHBBJMSA-N		Interactions Focus chain E [auth H] Interactions & Density Focus chain E [auth H]
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] Interactions & Density Focus chain D [auth H]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth H] MOL2 format, chain F [auth H] mmCIF format, chain F [auth H]	F [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth H] Interactions & Density Focus chain F [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth H] SDF format, chain H MOL2 format, chain G [auth H] MOL2 format, chain H mmCIF format, chain G [auth H] mmCIF format, chain H	G [auth H], H	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth H] Focus chain H Interactions & Density Focus chain G [auth H] Focus chain H

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS Query on TYS	C [auth I]	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
BJA	BindingDB: 3U98	Ki: min: 1.94, max: 3.5 (nM) from 2 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000877 (BJA) Query on PRD_000877	E [auth H]	(2S)-1-[(2R)-2-(BENZYLSULFONYLAMINO)-5-GUANIDINO-PENTANOYL]-N-[(4-CARBAMIMIDOYLPHENYL)METHYL]PYRROLIDINE-2-CARBOXAMIDE	Peptide-like / Thrombin inhibitor		Interactions Focus chain E [auth H] Interactions & Density Focus chain E [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.187
R-Value Work: 0.164
R-Value Observed: 0.165
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.3	α = 90
b = 71.5	β = 100.4
c = 72.2	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-10-24

Deposition Author(s):

Biela, A.

Heine, A.

Klebe, G.

Revision History (Full details and data files)

Version 1.0: 2012-10-24
Type: Initial release
Version 1.1: 2012-12-12
Changes: Other
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.4: 2023-12-06
Changes: Data collection
Version 1.5: 2024-10-16
Changes: Structure summary