5A2M | pdb_00005a2m

Thrombin Inhibitor

PDB DOI: https://doi.org/10.2210/pdb5A2M/pdb

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

Deposited: 2015-05-20 Released: 2016-06-01
Deposition Author(s): Ruehmann, E., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.159 (Depositor), 0.161 (DCC)
R-Value Work:
0.137 (Depositor), 0.141 (DCC)
R-Value Observed:
0.138 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

Literature

Thrombin Inhibition

Ruehmann, E., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 35.57 kDa
Atom Count: 2,672
Modeled Residue Count: 290
Deposited Residue Count: 299
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN HEAVY CHAIN	A [auth H]	258	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00734
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth H]	Go to GlyGen: P00734-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIRUDIN VARIANT-2	B [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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09945
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN LIGHT CHAIN	C [auth L]	29	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WX5 Query on WX5 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]	(2S)-1-[(2R)-5-carbamimidamido-2-[(phenylmethyl)sulfonylamino]pentanoyl]-N-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]pyrrolidine-2-carboxamide C₂₆ H₃₅ Cl N₆ O₅ S LWHZTVPXBHYWTP-PKTZIBPZSA-N		Interactions Focus chain G [auth H] Interactions & Density Focus chain G [auth H]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain H MOL2 format, chain H mmCIF 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
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [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] mmCIF format, chain E [auth H] mmCIF 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	B [auth I]	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.159 (Depositor), 0.161 (DCC)
R-Value Work: 0.137 (Depositor), 0.141 (DCC)
R-Value Observed: 0.138 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.114	α = 90
b = 71.242	β = 100.13
c = 72.368	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-06-01

Deposition Author(s):

Ruehmann, E.

Heine, A.

Klebe, G.

Revision History (Full details and data files)

Version 1.0: 2016-06-01
Type: Initial release
Version 2.0: 2019-10-23
Changes: Atomic model, Data collection, Derived calculations, Other
Version 2.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 2.2: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.3: 2024-11-20
Changes: Structure summary