8WUB | pdb_00008wub

The X-ray structure of human neuroglobin C120S mutant

PDB DOI: https://doi.org/10.2210/pdb8WUB/pdb

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

Deposited: 2023-10-20 Released: 2024-10-23
Deposition Author(s): Lin, Y.W., Yuan, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.204 (Depositor), 0.203 (DCC)
R-Value Work:
0.153 (Depositor), 0.154 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The X-ray structure of human neuroglobin C120S mutant

Lin, Y.W., Yuan, H.

To be published.

Macromolecule Content

Total Structure Weight: 53.23 kDa
Atom Count: 4,209
Modeled Residue Count: 437
Deposited Residue Count: 453
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuroglobin	A, B, C	151	Homo sapiens	Mutation(s): 1 Gene Names: NGB EC: 1.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPG2 (Homo sapiens) Explore Q9NPG2 Go to UniProtKB: Q9NPG2
PHAROS: Q9NPG2 GTEx: ENSG00000165553
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NPG2
Sequence Annotations Expand
Reference Sequence

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 D [auth A] SDF format, chain G [auth B] SDF format, chain K [auth C] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth C] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain K [auth C]	D [auth A], G [auth B], K [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain K [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain K [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C]	E [auth A] F [auth A] H [auth B] I [auth B] J [auth B] E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], L [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C]