7UF7 | pdb_00007uf7

Crystal structure of liganded Hb with the 5-HMF analog, MMA503

PDB DOI: https://doi.org/10.2210/pdb7UF7/pdb

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

Deposited: 2022-03-22 Released: 2022-03-30
Deposition Author(s): Donkor, A.K., Musayev, F.N., Safo, M.K.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.223 (Depositor), 0.222 (DCC)
R-Value Work:
0.157 (Depositor), 0.158 (DCC)
R-Value Observed:
0.161 (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

Improving the antisickling activity of furaldehyde

El-Araby, M.E., Omar, A.M., Ghatge, M.S., Musayev, F.N., Donkor, A.K., Paredes, S.D., Abdulmalik, O., Safo, M.K.

To be published.

Macromolecule Content

Total Structure Weight: 65.48 kDa
Atom Count: 5,370
Modeled Residue Count: 574
Deposited Residue Count: 578
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	142	Homo sapiens	Mutation(s): 0 Gene Names: HBA1, HBA2
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

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B, D	147	Homo sapiens	Mutation(s): 0 Gene Names: HBB
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 3 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 E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D]	E [auth A], H [auth B], J [auth C], M [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D]
N2Q (Subject of Investigation/LOI) Query on N2Q Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth C] MOL2 format, chain G [auth A] MOL2 format, chain L [auth C] mmCIF format, chain G [auth A] mmCIF format, chain L [auth C]	G [auth A], L [auth C]	(5P)-5-(5-methylfuran-2-yl)-1H-pyrazole C₈ H₈ N₂ O ZIJASYNQNLPMPY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth C] Interactions & Density Focus chain G [auth A] Focus chain L [auth C]
CMO (Subject of Investigation/LOI) Query on CMO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	F [auth A], I [auth B], K [auth C], N [auth D]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.223 (Depositor), 0.222 (DCC)
R-Value Work: 0.157 (Depositor), 0.158 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.614	α = 90
b = 83.12	β = 90
c = 105.122	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-30

Deposition Author(s):

Donkor, A.K.

Musayev, F.N.

Safo, M.K.

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R61HL156158
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	S10OD021756