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- PDB-4l7y: Deoxygenated Hb in complex with the allosteric effectors, IRL2500... -

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Basic information

Entry
Database: PDB / ID: 4l7y
TitleDeoxygenated Hb in complex with the allosteric effectors, IRL2500 and 2,3-DPG
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / alpha and beta subunits / heme
Function / homology
Function and homology information


cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(2R)-2,3-diphosphoglyceric acid / Chem-IRL / Mesoheme / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSafo, M.K. / Chowdhury, N.
CitationJournal: To be Published
Title: Novel small molecule modulators of human hemoglobin oxygen binding identified by small molecule microarray screening
Authors: Safo, M.K. / Chowdhury, N.
History
DepositionJun 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Other
Revision 1.2Jul 27, 2016Group: Non-polymer description
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,66911
Polymers62,0814
Non-polymers3,5887
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-21 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.750, 98.230, 65.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Hemoglobin subunit ... , 2 types, 4 molecules ACBD

#1: Protein Hemoglobin subunit alpha / / Alpha-globin / Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / / Beta-globin / Hemoglobin beta chain / LVV-hemorphin-7


Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 4 types, 655 molecules

#3: Chemical
ChemComp-MH0 / Mesoheme


Mass: 620.519 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H36FeN4O4
#4: Chemical ChemComp-IRL / (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)


Mass: 573.681 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H35N3O4
#5: Chemical ChemComp-DG2 / (2R)-2,3-diphosphoglyceric acid / 2,3-Bisphosphoglyceric acid / 2,3-bisphosphoglycerate / 2,3-BPG / 2,3-diphosphoglyceric acid / 2,3-diphosphoglycerate / 2,3-DPG / (2~{R})-2,3-diphosphonooxypropanoic acid / 2,3-Bisphosphoglyceric acid


Mass: 266.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O10P2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 648 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsIRL(202), DG2(202) AND DG2(203) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 297 K / Method: liquid diffusion / pH: 6.6
Details: 0.2M sodium acetate trihydrate, 0.1M sodium cacodylate trihydrate,30% PEG8000, pH 6.6, LIQUID DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 14, 2012 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→29.5 Å / Num. all: 53413 / Num. obs: 53413 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 30.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 8.4 / Num. unique all: 5004 / % possible all: 87.7

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HHB

2hhb


Resolution: 1.8→29.49 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1802166.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2706 5.1 %RANDOM
Rwork0.203 ---
obs0.203 53413 92.2 %-
all-53413 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4973 Å2 / ksol: 0.332242 e/Å3
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20 Å2
2--0.47 Å20 Å2
3----2.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 245 648 5263
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d18
X-RAY DIFFRACTIONc_improper_angle_d1.34
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.324 256 5.1 %
Rwork0.294 4748 -
obs--87.7 %

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