1C1J

STRUCTURE OF CADMIUM-SUBSTITUTED PHOSPHOLIPASE A2 FROM AGKISTRONDON HALYS PALLAS AT 2.8 ANGSTROMS RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb1C1J/pdb

Classification: HYDROLASE
Organism(s): Gloydius halys
Mutation(s): No

Deposited: 1999-07-22 Released: 2002-07-05
Deposition Author(s): Zhang, H.-l., Zhang, Y.-q., Song, S.-y., Zhou, Y., Lin, Z.-j.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.282 (Depositor), 0.278 (DCC)
R-Value Work:
0.201 (Depositor), 0.225 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure of Cadmium-substituted Phospholipase A2 from Agkistrodon halys Pallas at 2.8 Angstroms Resolution

Zhang, H.-l., Zhang, Y.-q., Song, S.-y., Zhou, Y., Lin, Z.-j.

(1999) Protein Pept Lett 6: 185-193

Macromolecule Content

Total Structure Weight: 56.95 kDa
Atom Count: 3,949
Modelled Residue Count: 488
Deposited Residue Count: 488
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BASIC PHOSPHOLIPASE A2	A, B, C, D	122	Gloydius halys	Mutation(s): 0 EC: 3.1.1.4
UniProt
Find proteins for O42187 (Gloydius halys) Explore O42187 Go to UniProtKB: O42187
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O42187
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D]	F [auth A] G [auth A] I [auth B] J [auth C] K [auth D] F [auth A], G [auth A], I [auth B], J [auth C], K [auth D], L [auth D]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.282 (Depositor), 0.278 (DCC)
R-Value Work: 0.201 (Depositor), 0.225 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.18	α = 90
b = 54.01	β = 111.59
c = 108.49	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2002-07-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-07-05
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Structure summary