7A0F

The Crystal Structure of Bovine Thrombin in complex with Hirudin (C22U/C39U) at 2.7 Angstroms Resolution

PDB DOI: https://doi.org/10.2210/pdb7A0F/pdb

Classification: HYDROLASE
Organism(s): Bos taurus, Hirudo medicinalis
Mutation(s): Yes

Deposited: 2020-08-07 Released: 2021-03-17
Deposition Author(s): Hidmi, T., Mousa, R., Pomyalov, S., Lansky, S., Khouri, L., Metanis, N., Shoham, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.253
R-Value Work: 0.194

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Diselenide crosslinks for enhanced and simplified oxidative protein folding

Mousa, R., Hidmi, T., Pomyalov, S., Lansky, S., Khouri, L., Shalev, D.E., Shoham, G., Metanis, N.

(2021) Commun Chem 4: 30

DOI: https://doi.org/10.1038/s42004-021-00463-9

Macromolecule Content

Total Structure Weight: 42.82 kDa
Atom Count: 2,936
Modelled Residue Count: 359
Deposited Residue Count: 373
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A [auth HHH]	259	Bos taurus	Mutation(s): 0 EC: 3.4.21.5
UniProt
Find proteins for P00735 (Bos taurus) Explore P00735 Go to UniProtKB: P00735
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00735
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth HHH]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin variant-1	B [auth III]	65	Hirudo medicinalis	Mutation(s): 2
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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	C [auth LLL]	49	Bos taurus	Mutation(s): 0 EC: 3.4.21.5
UniProt
Find proteins for P00735 (Bos taurus) Explore P00735 Go to UniProtKB: P00735
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00735
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth HHH] MOL2 format, chain D [auth HHH] mmCIF format, chain D [auth HHH]	D [auth HHH]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth HHH] Interactions & Density Focus chain D [auth HHH]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth HHH] MOL2 format, chain E [auth HHH] mmCIF format, chain E [auth HHH]	E [auth HHH]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth HHH] Interactions & Density Focus chain E [auth HHH]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.253
R-Value Work: 0.194
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.069	α = 90
b = 101.498	β = 90
c = 142.075	γ = 90

Software Package:

Software Name	Purpose
XDS	data processing
Aimless	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-03-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-03-17
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary