3PT8 | pdb_00003pt8

Structure of HbII-III-CN from Lucina pectinata at pH 5.0

PDB DOI: https://doi.org/10.2210/pdb3PT8/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Phacoides pectinatus
Mutation(s): Yes

Deposited: 2010-12-02 Released: 2011-12-07
Deposition Author(s): Gavira, J.A., Ruiz-Martinez, C.R., Nieves-Marrero, C.A., Estremera-Andujar, R.A., Lopez-Garriga, J., Garcia-Ruiz, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.226 (Depositor), 0.226 (DCC)
R-Value Work:
0.197 (Depositor), 0.194 (DCC)
R-Value Observed:
0.198 (Depositor)

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

New Crystallographic Structure of HbII-III-Oxy and CN forms from Lucina pectinata.

Ruiz-Martinez, C.R., Nieves-Marrero, C.A., Estremera-Andujar, R.A., Lopez-Garriga, J., Garcia-Ruiz, J.M., Gavira, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 36.11 kDa
Atom Count: 2,872
Modeled Residue Count: 304
Deposited Residue Count: 304
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin II	A	152	Phacoides pectinatus	Mutation(s): 1
UniProt
Find proteins for P41261 (Phacoides pectinatus) Explore P41261 Go to UniProtKB: P41261
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41261
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin III	B	152	Phacoides pectinatus	Mutation(s): 0
UniProt
Find proteins for P41262 (Phacoides pectinatus) Explore P41262 Go to UniProtKB: P41262
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41262
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], K [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B]
CYN Query on CYN Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.226 (Depositor), 0.226 (DCC)
R-Value Work: 0.197 (Depositor), 0.194 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.231	α = 90
b = 74.231	β = 90
c = 152.302	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-12-07

Deposition Author(s):

Gavira, J.A.

Ruiz-Martinez, C.R.

Nieves-Marrero, C.A.

Estremera-Andujar, R.A.

Lopez-Garriga, J.

Garcia-Ruiz, J.M.

Revision History (Full details and data files)

Version 1.0: 2011-12-07
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary