6YB6

Thrombin in complex with D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative (13c)

PDB DOI: https://doi.org/10.2210/pdb6YB6/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens, Hirudo medicinalis, synthetic construct
Mutation(s): No

Deposited: 2020-03-16 Released: 2021-03-31
Deposition Author(s): Sandner, A., Heine, A., Klebe, G., Abazi, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.153
R-Value Work: 0.131
R-Value Observed: 0.132

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Thrombin in complex with D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative (13c)

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

To be published.

Macromolecule Content

Total Structure Weight: 36.36 kDa
Atom Count: 2,799
Modelled Residue Count: 292
Deposited Residue Count: 310
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	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
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
Prothrombin	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
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

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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% Identity50% Identity70% Identity90% Identity95% Identity100% 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
D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative	D	3	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H MOL2 format, chain H	H	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H Interactions & Density Focus chain H
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain I [auth H] MOL2 format, chain I [auth H]	I [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth H] Interactions & Density Focus chain I [auth H]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain G [auth H] SDF format, chain J [auth H] MOL2 format, chain G [auth H] MOL2 format, chain J [auth H]	G [auth H], J [auth H]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth H] Focus chain J [auth H] Interactions & Density Focus chain G [auth H] Focus chain J [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain F [auth H] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H]	E [auth H], F [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Interactions & Density Focus chain E [auth H] Focus chain F [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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.153
R-Value Work: 0.131
R-Value Observed: 0.132
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.436	α = 90
b = 71.2	β = 100.2
c = 72.316	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
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: 2021-03-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-03-31
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 2.0: 2024-07-24
Changes: Advisory, Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary