8V8F | pdb_00008v8f

The co-crystal structure of anti-HIV scFv and Utag

PDB DOI: https://doi.org/10.2210/pdb8V8F/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Mus musculus, Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-12-05 Released: 2024-12-11
Deposition Author(s): Chen, S.H., Snow, C.D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.275 (Depositor), 0.275 (DCC)
R-Value Work:
0.225 (Depositor), 0.226 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

anti-HIV protease intracellular antibody scFv

Zhao, N., Stasevich, T., Chen, S.H., Snow, C.D.

To be published.

Macromolecule Content

Total Structure Weight: 123.69 kDa
Atom Count: 7,865
Modeled Residue Count: 996
Deposited Residue Count: 1,152
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-HIV scFv	A [auth B], B [auth A], C, D	277	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Utag	E, F, G, H	11	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth E] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E]	I [auth B] J [auth B] K [auth A] L [auth A] M [auth A] I [auth B], J [auth B], K [auth A], L [auth A], M [auth A], N [auth C], O [auth D], P [auth D], Q [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.275 (Depositor), 0.275 (DCC)
R-Value Work: 0.225 (Depositor), 0.226 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.467	α = 68.834
b = 61.824	β = 77.898
c = 85.577	γ = 71.375

Software Package:

Software Name	Purpose
PHENIX	refinement
pointless	data scaling
XDS	data reduction
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-12-11

Deposition Author(s):

Chen, S.H.

Snow, C.D.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R56AI155897
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R01AI168459-01A1

Revision History (Full details and data files)

Version 1.0: 2024-12-11
Type: Initial release
Version 2.0: 2025-05-07
Type: Coordinate replacement
Reason: Model orientation/position
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary