3R5I

Crystal structure of liganded Hemoglobin complexed with a potent Antisickling agent, INN-312

PDB DOI: https://doi.org/10.2210/pdb3R5I/pdb

Classification: oxygen transport, oxygen binding
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2011-03-18 Released: 2011-04-06
Deposition Author(s): Safo, M.K., Musayev, F.N., Safo, R.P., Daniels, D., Eseonu, D.N., Parra, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.268
R-Value Work: 0.209
R-Value Observed: 0.212

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

Structural and in Vitro Chracterization of Pyridyl Derivatives of Benzaldehydes : Highly Potent Antisickling Agents

Abulmalik, O., Ghatge, M.S., Nnamani, I., Eseonu, D.N., Musayev, F.N., Danso-Danquah, R., Venitz, J., Asakura, T., Abraham, D.J., Safo, M.K.

To be published.

Macromolecule Content

Total Structure Weight: 65.69 kDa
Atom Count: 4,940
Modelled Residue Count: 574
Deposited Residue Count: 574
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A, C	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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B, D	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 F [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	F [auth A], J [auth B], N [auth C], Q [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D]
3R5 Query on 3R5 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth C]	G [auth A], H [auth A], O [auth C]	5-methoxy-2-(pyridin-3-ylmethoxy)benzaldehyde C₁₄ H₁₃ N O₃ GXQNKVDAAINMNE-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain R [auth D] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain R [auth D] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain R [auth D]	K [auth B], L [auth B], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth D] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth D]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	E [auth A], I [auth B], M [auth C], P [auth D]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.268
R-Value Work: 0.209
R-Value Observed: 0.212
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.1	α = 90
b = 92.1	β = 90
c = 143.788	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-04-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-04-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-27
Changes: Structure summary