3B75 | pdb_00003b75

Crystal Structure of Glycated Human Haemoglobin

PDB DOI: https://doi.org/10.2210/pdb3B75/pdb

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

Deposited: 2007-10-30 Released: 2008-10-14
Deposition Author(s): Saraswathi, N.T., Syakhovich, V.E., Bokut, S.B., Moras, D., Ruff, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.331 (Depositor), 0.328 (DCC)
R-Value Work:
0.244 (Depositor), 0.243 (DCC)
R-Value Observed:
0.249 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

The effect of hemoglobin glycosylation on diabete linked oxidative stress

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

To be published.

Macromolecule Content

Total Structure Weight: 162.68 kDa
Atom Count: 11,931
Modeled Residue Count: 1,435
Deposited Residue Count: 1,435
Unique protein chains: 2

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69905
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68871
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain FA [auth S] SDF format, chain O [auth B] SDF format, chain W [auth E] SDF format, chain Y [auth F] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain L [auth A] SDF format, chain IA [auth T] SDF format, chain DA [auth H] SDF format, chain BA [auth G] MOL2 format, chain FA [auth S] MOL2 format, chain O [auth B] MOL2 format, chain W [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain L [auth A] MOL2 format, chain IA [auth T] MOL2 format, chain DA [auth H] MOL2 format, chain BA [auth G] mmCIF format, chain FA [auth S] mmCIF format, chain O [auth B] mmCIF format, chain W [auth E] mmCIF format, chain Y [auth F] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain L [auth A] mmCIF format, chain IA [auth T] mmCIF format, chain DA [auth H] mmCIF format, chain BA [auth G]	BA [auth G] DA [auth H] FA [auth S] IA [auth T] L [auth A] BA [auth G], DA [auth H], FA [auth S], IA [auth T], L [auth A], O [auth B], R [auth C], T [auth D], W [auth E], Y [auth F]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain BA [auth G] Focus chain DA [auth H] Focus chain FA [auth S] Focus chain IA [auth T] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain DA [auth H] Focus chain FA [auth S] Focus chain IA [auth T] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Y [auth F]
FRU Query on FRU Download:Ideal Coordinates CCD File SDF format, chain V [auth E] SDF format, chain K [auth A] MOL2 format, chain V [auth E] MOL2 format, chain K [auth A] mmCIF format, chain V [auth E] mmCIF format, chain K [auth A]	K [auth A], V [auth E]	beta-D-fructofuranose C₆ H₁₂ O₆ RFSUNEUAIZKAJO-ARQDHWQXSA-N		Interactions Focus chain K [auth A] Focus chain V [auth E] Interactions & Density Focus chain K [auth A] Focus chain V [auth E]
GLC Query on GLC Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain HA [auth T] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain HA [auth T] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain HA [auth T]	HA [auth T], N [auth B], Q [auth C]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain HA [auth T] Focus chain N [auth B] Focus chain Q [auth C] Interactions & Density Focus chain HA [auth T] Focus chain N [auth B] Focus chain Q [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] MOL2 format, chain AA [auth G] mmCIF format, chain AA [auth G]	AA [auth G]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth G] Interactions & Density Focus chain AA [auth G]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain EA [auth H] SDF format, chain X [auth E] SDF format, chain Z [auth F] SDF format, chain U [auth D] SDF format, chain S [auth C] SDF format, chain P [auth B] SDF format, chain M [auth A] SDF format, chain JA [auth T] SDF format, chain GA [auth S] SDF format, chain CA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain U [auth D] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] MOL2 format, chain M [auth A] MOL2 format, chain JA [auth T] MOL2 format, chain GA [auth S] MOL2 format, chain CA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain X [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain U [auth D] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B] mmCIF format, chain M [auth A] mmCIF format, chain JA [auth T] mmCIF format, chain GA [auth S] mmCIF format, chain CA [auth G]	CA [auth G] EA [auth H] GA [auth S] JA [auth T] M [auth A] CA [auth G], EA [auth H], GA [auth S], JA [auth T], M [auth A], P [auth B], S [auth C], U [auth D], X [auth E], Z [auth F]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain EA [auth H] Focus chain GA [auth S] Focus chain JA [auth T] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain EA [auth H] Focus chain GA [auth S] Focus chain JA [auth T] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain X [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.331 (Depositor), 0.328 (DCC)
R-Value Work: 0.244 (Depositor), 0.243 (DCC)
R-Value Observed: 0.249 (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
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-10-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-10-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 1.4: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.5: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary