4MQK | pdb_00004mqk

Carbonmonoxy Structure of the Human Fetal Hemoglobin Mutant HbF Toms River alphawtgammaV67M

PDB DOI: https://doi.org/10.2210/pdb4MQK/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-09-16 Released: 2013-10-30
Deposition Author(s): Soman, J., Olson, J.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.175 (Depositor), 0.180 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Carbonmonoxy Structure of the Human Fetal Hemoglobin Mutant HbF Toms River alphawtgammaV67M

Soman, J., Olson, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 129.9 kDa
Atom Count: 9,377
Modelled Residue Count: 1,140
Deposited Residue Count: 1,148
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A, C, E, G	141	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69905
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit gamma-2	B, D, F, H	146	Homo sapiens	Mutation(s): 1 Gene Names: HBB, HBG2
UniProt & NIH Common Fund Data Resources
Find proteins for P69892 (Homo sapiens) Explore P69892 Go to UniProtKB: P69892
PHAROS: P69892 GTEx: ENSG00000196565
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69892
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth F] SDF format, chain T [auth G] SDF format, chain U [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain T [auth G] MOL2 format, chain U [auth H] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F] mmCIF format, chain T [auth G] mmCIF format, chain U [auth H]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], R [auth F], T [auth G], U [auth H]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain T [auth G] Focus chain U [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain T [auth G] Focus chain U [auth H]
CMO Query on CMO Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain S [auth F] SDF format, chain V [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain S [auth F] MOL2 format, chain V [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain S [auth F] mmCIF format, chain V [auth H]	J [auth A] L [auth B] N [auth C] P [auth D] S [auth F] J [auth A], L [auth B], N [auth C], P [auth D], S [auth F], V [auth H]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth F] Focus chain V [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth F] Focus chain V [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.175 (Depositor), 0.180 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.04	α = 90
b = 52.229	β = 114.27
c = 106.381	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-10-30

Deposition Author(s):

Soman, J.

Olson, J.S.

Revision History (Full details and data files)

Version 1.0: 2013-10-30
Type: Initial release
Version 1.1: 2013-11-06
Changes: Other
Version 1.2: 2014-10-08
Changes: Database references
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations

Prepare Data

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Deposit Data

Help and Resources

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Carbonmonoxy Structure of the Human Fetal Hemoglobin Mutant HbF Toms River alphawtgammaV67M

Carbonmonoxy Structure of the Human Fetal Hemoglobin Mutant HbF Toms River alphawtgammaV67M

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

4MQK | pdb_00004mqk