5MLS

Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(3-chlorobenzyl)pyrrolidine-2-carboxamide

PDB DOI: https://doi.org/10.2210/pdb5MLS/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens, Hirudo medicinalis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-12-07 Released: 2017-12-20
Deposition Author(s): Marca, A., Sandner, A., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.180
R-Value Work: 0.160
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Thrombin Mutante A190S in complex with (S)-1-((R)-2-amino-3,3-diphenylpropanoyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide

Marca, A., Sandner, A., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 36.6 kDa
Atom Count: 2,620
Modelled Residue Count: 289
Deposited Residue Count: 307
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 Gene Names: F2 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): 1 Gene Names: F2 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 D]	12	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
22U Query on 22U 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]	D-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide C₂₁ H₂₄ Cl N₃ O₂ CJHLRGCXPGIPCB-MOPGFXCFSA-N		Interactions 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]
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] SDF format, chain J [auth H] SDF format, chain K [auth H] SDF format, chain L [auth H] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H]	G [auth H] H I [auth H] J [auth H] K [auth H] G [auth H], H, I [auth H], J [auth H], K [auth H], L [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H]
DMS Query on DMS 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]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain M [auth H] SDF format, chain N [auth H] MOL2 format, chain M [auth H] MOL2 format, chain N [auth H] mmCIF format, chain M [auth H] mmCIF format, chain N [auth H]	M [auth H], N [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth H] Focus chain N [auth H]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
22U	BindingDB: 5MLS	Ki: min: 90, max: 250 (nM) from 3 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000593 (22U) Query on PRD_000593	D [auth H]	D-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide	Peptide-like / Thrombin inhibitor		Interactions Focus chain D [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.180
R-Value Work: 0.160
R-Value Observed: 0.160
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.417	α = 90
b = 71.597	β = 100.58
c = 73.069	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 1.1: 2018-06-13
Changes: Data collection, Structure summary
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary