3DSL

The Three-dimensional Structure of Bothropasin, the Main Hemorrhagic Factor from Bothrops jararaca venom.

PDB DOI: https://doi.org/10.2210/pdb3DSL/pdb

Classification: HYDROLASE
Organism(s): Bothrops jararaca
Mutation(s): No

Deposited: 2008-07-13 Released: 2008-10-21
Deposition Author(s): Muniz, J.R.C., Ambrosio, A., Selistre-de-Araujo, H.S., Oliva, G., Garratt, R.C., Souza, D.H.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.294
R-Value Work: 0.210
R-Value Observed: 0.217

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 94.82 kDa
Atom Count: 6,675
Modelled Residue Count: 828
Deposited Residue Count: 838
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc metalloproteinase-disintegrin bothropasin	A, B	419	Bothrops jararaca	Mutation(s): 0 EC: 3.4.24.49
UniProt
Find proteins for O93523 (Bothrops jararaca) Explore O93523 Go to UniProtKB: O93523
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O93523
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLE Query on FLE Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A]	H [auth A], J [auth A]	FUROYL-LEUCINE C₁₁ H₁₅ N O₄ LXBURZIESWDWIV-QMMMGPOBSA-N		Interactions Focus chain H [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain J [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
TRP Query on TRP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A]	I [auth A], K [auth A]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain I [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain K [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B]	G [auth A], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain O [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	D [auth A] E [auth A] F [auth A] L [auth B] M [auth B] D [auth A], E [auth A], F [auth A], L [auth B], M [auth B], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.294
R-Value Work: 0.210
R-Value Observed: 0.217
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.757	α = 90
b = 100.271	β = 90
c = 133.237	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystalClear	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-10-21

Deposition Author(s):

Muniz, J.R.C.

Ambrosio, A.

Selistre-de-Araujo, H.S.

Oliva, G.

Garratt, R.C.

Souza, D.H.F.

Revision History (Full details and data files)

Version 1.0: 2008-10-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary

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3DSL

The Three-dimensional Structure of Bothropasin, the Main Hemorrhagic Factor from Bothrops jararaca venom.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)