2ZDV | pdb_00002zdv

Exploring Thrombin S1 pocket

PDB DOI: https://doi.org/10.2210/pdb2ZDV/pdb

Classification: Blood Clotting/Hydrolase Inhibitor
Organism(s): Homo sapiens, Hirudo medicinalis
Mutation(s): No

Deposited: 2007-11-29 Released: 2008-10-28
Deposition Author(s): Baum, B., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.243 (Depositor), 0.200 (DCC)
R-Value Work:
0.187 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.7 of the entry. See complete history.

Literature

Exploring Thrombin S1 pocket

Baum, B., Hangauer, D., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 35.81 kDa
Atom Count: 2,602
Modeled Residue Count: 289
Deposited Residue Count: 306
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(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

Find similar proteins by:

(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-1	C [auth I]	11	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P01050 (Hirudo medicinalis) Explore P01050 Go to UniProtKB: P01050
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01050
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
37U Query on 37U Download Ideal Coordinates CCD File SDF format, chain G [auth H] MOL2 format, chain G [auth H] mmCIF format, chain G [auth H]	G [auth H]	D-phenylalanyl-N-(3-fluorobenzyl)-L-prolinamide C₂₁ H₂₄ F N₃ O₂ JGZSVYZIJHGHMA-MOPGFXCFSA-N		Interactions Focus chain G [auth H] Interactions & Density Focus chain G [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 E [auth H] SDF format, chain D [auth H] MOL2 format, chain E [auth H] MOL2 format, chain D [auth H] mmCIF format, chain E [auth H] mmCIF format, chain D [auth H]	D [auth H], E [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain E [auth H] Interactions & Density Focus chain D [auth H] Focus chain E [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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 6
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000602 (37U) Query on PRD_000602	G [auth H]	D-phenylalanyl-N-(3-fluorobenzyl)-L-prolinamide	Peptide-like / Thrombin inhibitor		Interactions Focus chain G [auth H] Interactions & Density Focus chain G [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.243 (Depositor), 0.200 (DCC)
R-Value Work: 0.187 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.5	α = 90
b = 71.4	β = 100.6
c = 72.8	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-10-28

Deposition Author(s):

Baum, B.

Heine, A.

Klebe, G.

Revision History (Full details and data files)

Version 1.0: 2008-10-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.2: 2012-12-12
Changes: Other
Version 1.3: 2016-05-25
Changes: Source and taxonomy
Version 1.4: 2017-10-11
Changes: Refinement description
Version 1.5: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.6: 2023-11-15
Changes: Data collection
Version 1.7: 2024-10-30
Changes: Structure summary