8FDM

Human Hemoglobin in Complex with Nitrosomethane

PDB DOI: https://doi.org/10.2210/pdb8FDM/pdb

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

Deposited: 2022-12-03 Released: 2023-07-12
Deposition Author(s): Powell, S.M., Richter-Addo, G.B., Thomas, L.M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.253
R-Value Work: 0.196
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structural investigations of heme protein derivatives resulting from reactions of aryl- and alkylhydroxylamines with human hemoglobin

Powell, S.M., Wang, B., Herrera, V.E., Prather, K.Y., Nguyen, N.T., Abucayon, E.G., Thomas, L.M., Safo, M.K., Richter-Addo, G.B.

(2023) J Inorg Biochem 246: 112304

DOI: https://doi.org/10.1016/j.jinorgbio.2023.112304

Macromolecule Content

Total Structure Weight: 65.38 kDa
Atom Count: 4,794
Modelled Residue Count: 570
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D]	E [auth A], J [auth B], M [auth C], Q [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C]	P [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
MBN (Subject of Investigation/LOI) Query on MBN Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth C] MOL2 format, chain H [auth A] MOL2 format, chain O [auth C]	H [auth A], O [auth C]	TOLUENE C₇ H₈ YXFVVABEGXRONW-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth C] Interactions & Density Focus chain H [auth A] Focus chain O [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B]	F [auth A], G [auth A], I [auth A], L [auth B], N [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C]
NSM Query on NSM Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain R [auth D] MOL2 format, chain K [auth B] MOL2 format, chain R [auth D]	K [auth B], R [auth D]	NITROSOMETHANE C H₃ N O IMHRONYAKYWGCC-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain R [auth D] Interactions & Density Focus chain K [auth B] Focus chain R [auth D]