3CIU | pdb_00003ciu

Site-Selective Glycosylation of Cysteine-93 beta on the Surface of Bovine Hemoglobin and its Application as a Novel Oxygen Therapeutic

PDB DOI: https://doi.org/10.2210/pdb3CIU/pdb

Classification: OXYGEN BINDING
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2008-03-11 Released: 2008-04-15
Deposition Author(s): Bhatt, V.S., Zhang, Y., Sun, G., Wang, P.G., Palmer, A.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.332 (Depositor), 0.298 (DCC)
R-Value Work:
0.268 (Depositor), 0.254 (DCC)
R-Value Observed:
0.271 (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

Site-Selective Glycosylation of Cysteine-93 beta on the Surface of Bovine Hemoglobin and its Application as a Novel Oxygen Therapeutic

Bhatt, V.S., Zhang, Y., Sun, G., Wang, P.G., Palmer, A.F.

To be published.

Macromolecule Content

Total Structure Weight: 65.29 kDa
Atom Count: 4,579
Modeled Residue Count: 571
Deposited Residue Count: 572
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	Bos taurus	Mutation(s): 0 Gene Names: HBA
UniProt
Find proteins for P01966 (Bos taurus) Explore P01966 Go to UniProtKB: P01966
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01966
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B, D	145	Bos taurus	Mutation(s): 0 Gene Names: HBB
UniProt
Find proteins for P02070 (Bos taurus) Explore P02070 Go to UniProtKB: P02070
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02070
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5DP Query on 5DP Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	5-(2,5-dioxopyrrolidin-1-yl)-N-[2-(2-{2-[(4-O-alpha-D-idopyranosyl-alpha-D-mannopyranosyl)oxy]ethoxy}ethoxy)ethyl]pentanamide C₂₇ H₄₆ N₂ O₁₆ GIIWJKKPIBKANP-SLHLUNFVSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], J [auth C], L [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
O Query on O Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], K [auth C], M [auth D]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.332 (Depositor), 0.298 (DCC)
R-Value Work: 0.268 (Depositor), 0.254 (DCC)
R-Value Observed: 0.271 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.604	α = 90
b = 73.982	β = 90
c = 129.796	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-04-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-04-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary