5HY8 | pdb_00005hy8

Glycation restrains allosteric transition in hemoglobin: The molecular basis of oxidative stress under hyperglycemic conditions in diabetes

PDB DOI: https://doi.org/10.2210/pdb5HY8/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2016-02-01 Released: 2017-02-01
Deposition Author(s): Saraswathi, N.T., Pannu, N.S., Syakhovich, V.E., Saurabh, A., Bokut, S.B., Moras, D., Ruff, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.244 (Depositor), 0.287 (DCC)
R-Value Work:
0.203 (Depositor), 0.258 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Glycation restrains allosteric transition in hemoglobin: The molecular basis of oxidative stress under hyperglycemic conditions in diabetes

Saraswathi, N.T., Pannu, N.S., Syakhovich, V.E., Saurabh, A., Bokut, S.B., Moras, D., Ruff, M.

To be published.

Macromolecule Content

Total Structure Weight: 162.34 kDa
Atom Count: 11,609
Modeled Residue Count: 1,428
Deposited Residue Count: 1,435
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A, C, E, G, I [auth S]	141	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905 Go to UniProtKB: P69905
PHAROS: P69905 GTEx: ENSG00000188536 ENSG00000206172
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69905
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B, D, F, H, J [auth T]	146	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871 Go to UniProtKB: P68871
PHAROS: P68871 GTEx: ENSG00000244734
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68871
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 BA [auth H] SDF format, chain CA [auth S] SDF format, chain EA [auth T] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain W [auth F] SDF format, chain Z [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth S] MOL2 format, chain EA [auth T] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Z [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain CA [auth S] mmCIF format, chain EA [auth T] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Z [auth G]	BA [auth H] CA [auth S] EA [auth T] K [auth A] N [auth B] BA [auth H], CA [auth S], EA [auth T], K [auth A], N [auth B], P [auth C], T [auth D], V [auth E], W [auth F], Z [auth G]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain BA [auth H] Focus chain CA [auth S] Focus chain EA [auth T] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain CA [auth S] Focus chain EA [auth T] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth F] Focus chain Z [auth G]
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain S [auth C] MOL2 format, chain S [auth C] mmCIF format, chain S [auth C]	S [auth C]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain S [auth C] Interactions & Density Focus chain S [auth C]
FRU Query on FRU Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain R [auth C] SDF format, chain Y [auth F] MOL2 format, chain M [auth A] MOL2 format, chain R [auth C] MOL2 format, chain Y [auth F] mmCIF format, chain M [auth A] mmCIF format, chain R [auth C] mmCIF format, chain Y [auth F]	M [auth A], R [auth C], Y [auth F]	beta-D-fructofuranose C₆ H₁₂ O₆ RFSUNEUAIZKAJO-ARQDHWQXSA-N		Interactions Focus chain M [auth A] Focus chain R [auth C] Focus chain Y [auth F] Interactions & Density Focus chain M [auth A] Focus chain R [auth C] Focus chain Y [auth F]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain DA [auth S] SDF format, chain FA [auth T] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain X [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain DA [auth S] MOL2 format, chain FA [auth T] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain DA [auth S] mmCIF format, chain FA [auth T] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain X [auth F]	AA [auth G] DA [auth S] FA [auth T] L [auth A] O [auth B] AA [auth G], DA [auth S], FA [auth T], L [auth A], O [auth B], Q [auth C], U [auth D], X [auth F]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain DA [auth S] Focus chain FA [auth T] Focus chain L [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth S] Focus chain FA [auth T] Focus chain L [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.244 (Depositor), 0.287 (DCC)
R-Value Work: 0.203 (Depositor), 0.258 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 237.987	α = 90
b = 59.267	β = 125.36
c = 137.024	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-02-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-02-01
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2025-10-01
Changes: Advisory, Derived calculations, Structure summary