3RLW

Human Thrombin in complex with MI328

PDB DOI: https://doi.org/10.2210/pdb3RLW/pdb

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

Deposited: 2011-04-20 Released: 2012-04-25
Deposition Author(s): Biela, A., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.192
R-Value Work: 0.163
R-Value Observed: 0.164

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 36.64 kDa
Atom Count: 2,718
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
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S28 Query on S28 Download Ideal Coordinates CCD File SDF format, chain E [auth H] MOL2 format, chain E [auth H]	E [auth H]	N-(benzylsulfonyl)glycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide C₂₂ H₂₇ N₅ O₄ S CEBNOQRCTYYHRQ-IBGZPJMESA-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]	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]	F [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth H] Interactions & Density Focus chain F [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth H] SDF format, chain H SDF format, chain I [auth H] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth H]	G [auth H], H, I [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth H] Focus chain H Focus chain I [auth H] Interactions & Density Focus chain G [auth H] Focus chain H Focus chain I [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth H] SDF format, chain K [auth H] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H]	J [auth H], K [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth H] Focus chain K [auth H] Interactions & Density Focus chain J [auth H] Focus chain K [auth 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
S28	BindingDB: 3RLW	Ki: 3.7 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001087 (S28) Query on PRD_001087	E [auth H]	N-(BENZYLSULFONYL)GLYCYL-N-(4-CARBAMIMIDOYLBENZYL)-L-PROLINAMIDE	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: 1.69 Å
R-Value Free: 0.192
R-Value Work: 0.163
R-Value Observed: 0.164
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.5	α = 90
b = 71.3	β = 100.6
c = 72.5	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: 2012-04-25

Deposition Author(s):

Biela, A.

Heine, A.

Klebe, G.

Revision History (Full details and data files)

Version 1.0: 2012-04-25
Type: Initial release
Version 1.1: 2012-12-12
Changes: Other
Version 1.2: 2016-07-13
Changes: Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.5: 2023-12-06
Changes: Data collection

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Deposit Data

Help and Resources

3RLW

Human Thrombin in complex with MI328

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 5

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)