4L7Y | pdb_00004l7y

Deoxygenated Hb in complex with the allosteric effectors, IRL2500 and 2,3-DPG

PDB DOI: https://doi.org/10.2210/pdb4L7Y/pdb

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

Deposited: 2013-06-14 Released: 2013-07-03
Deposition Author(s): Safo, M.K., Chowdhury, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.228 (Depositor), 0.217 (DCC)
R-Value Work:
0.203 (Depositor), 0.193 (DCC)
R-Value Observed:
0.203 (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

Novel small molecule modulators of human hemoglobin oxygen binding identified by small molecule microarray screening

Safo, M.K., Chowdhury, N.

To be published.

Macromolecule Content

Total Structure Weight: 65.67 kDa
Atom Count: 5,263
Modeled Residue Count: 572
Deposited Residue Count: 574
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	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

Find similar proteins by:

| 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% 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
MH0 Query on MH0 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain H [auth C] SDF format, chain I [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth C] mmCIF format, chain I [auth D]	E [auth A], F [auth B], H [auth C], I [auth D]	Mesoheme C₃₄ H₃₆ Fe N₄ O₄ CKMCSMAXNUVLQI-RGGAHWMASA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain I [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain I [auth D]
IRL Query on IRL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	(2R)-2-({(2S)-3-(biphenyl-4-yl)-2-[(3,5-dimethylbenzoyl)(methyl)amino]propanoyl}amino)-3-(1H-indol-3-yl)propanoic acid (non-preferred name) C₃₆ H₃₅ N₃ O₄ UZDORQWMYRRLQV-SAIUNTKASA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
DG2 Query on DG2 Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D]	J [auth D], K [auth D]	(2R)-2,3-diphosphoglyceric acid C₃ H₈ O₁₀ P₂ XOHUEYCVLUUEJJ-UWTATZPHSA-N		Interactions Focus chain J [auth D] Focus chain K [auth D] Interactions & Density Focus chain J [auth D] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.228 (Depositor), 0.217 (DCC)
R-Value Work: 0.203 (Depositor), 0.193 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.75	α = 90
b = 98.23	β = 90
c = 65.34	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-07-03

Deposition Author(s):

Safo, M.K.

Chowdhury, N.

Revision History (Full details and data files)

Version 1.0: 2013-07-03
Type: Initial release
Version 1.1: 2014-04-16
Changes: Other
Version 1.2: 2016-07-27
Changes: Non-polymer description
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description