5XRF | pdb_00005xrf

Crystal structure of Da-36, a thrombin-like enzyme from Deinagkistrodon acutus

PDB DOI: https://doi.org/10.2210/pdb5XRF/pdb

Classification: HYDROLASE
Organism(s): Deinagkistrodon acutus
Mutation(s): No

Deposited: 2017-06-08 Released: 2018-06-13
Deposition Author(s): Lin, C.-C., Wu, W.-G., Fan, Q., Tian, J., Zhang, Z., Zheng, Y.
Funding Organization(s): Yunnan Provincial Science and Technology Department

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.193 (Depositor), 0.197 (DCC)
R-Value Work:
0.179 (Depositor), 0.183 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of Da-36, a thrombin-like enzyme from Deinagkistrodon acutus

Fan, Q., Tian, J., Zhang, Z., Lin, C.-C., Wu, W.-G., Zheng, Y.

To be published.

Macromolecule Content

Total Structure Weight: 28.79 kDa
Atom Count: 2,219
Modeled Residue Count: 236
Deposited Residue Count: 242
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Snake venom serine protease Da-36	A	242	Deinagkistrodon acutus	Mutation(s): 0
UniProt
Find proteins for J7LCB0 (Deinagkistrodon acutus) Explore J7LCB0 Go to UniProtKB: J7LCB0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	J7LCB0
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G00395TQ GlyCosmos: G00395TQ GlyGen: G00395TQ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.193 (Depositor), 0.197 (DCC)
R-Value Work: 0.179 (Depositor), 0.183 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.481	α = 90
b = 87.481	β = 90
c = 104.674	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-06-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Yunnan Provincial Science and Technology Department	China	2013FA060

Revision History (Full details and data files)

Version 1.0: 2018-06-13
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-06
Changes: Structure summary