9JYU | pdb_00009jyu

Structural analysis of yak hemoglobin

PDB DOI: https://doi.org/10.2210/pdb9JYU/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Bos grunniens
Mutation(s): No

Deposited: 2024-10-12 Released: 2026-01-28
Deposition Author(s): Dachuan, Y., Xiaoqian, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free:
0.282 (Depositor), 0.283 (DCC)
R-Value Work:
0.240 (Depositor), 0.240 (DCC)
R-Value Observed:
0.242 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 9JYU

This is version 1.0 of the entry. See complete history.

Literature

Interface sliding as illustrated by the multiple quaternary structures of liganded hemoglobin.

Dachuan, Y., Xiaoqian, J.

To be published.

Macromolecule Content

Total Structure Weight: 64.59 kDa
Atom Count: 5,020
Modeled Residue Count: 572
Deposited Residue Count: 572
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha-2	A, C	141	Bos grunniens	Mutation(s): 0
UniProt
Find proteins for P01968 (Bos mutus grunniens) Explore P01968 Go to UniProtKB: P01968
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01968
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B, D	145	Bos grunniens	Mutation(s): 0
UniProt
Find proteins for P02072 (Bos mutus grunniens) Explore P02072 Go to UniProtKB: P02072
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02072
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], J [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth D]
CMO (Subject of Investigation/LOI) Query on CMO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain K [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth D]	F [auth A], H [auth B], K [auth D]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.282 (Depositor), 0.283 (DCC)
R-Value Work: 0.240 (Depositor), 0.240 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.485	α = 90
b = 77.295	β = 90
c = 108.595	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-01-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82172063

Revision History (Full details and data files)

Version 1.0: 2026-01-28
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.