5GIK | pdb_00005gik

Modulation of the affinity of a HIV-1 capsid-directed ankyrin towards its viral target through critical amino acid editing

PDB DOI: https://doi.org/10.2210/pdb5GIK/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-06-24 Released: 2017-06-28
Deposition Author(s): Chuankhayan, P., Saoin, S., Wisitponchai, T., Intachai, K., Chupradit, K., Moonmuang, S., Kitidee, K., Nangola, S., Sanghiran, L.V., Hong, S.S., Boulanger, P., Tayapiwatana, C., Chen, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.187 (Depositor), 0.190 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Modulation of the affinity of a HIV-1 capsid-directed ankyrintowards its viral target through critical amino acid editing

Chuankhayan, P., Saoin, S., Wisitponchai, T., Intachai, K., Chupradit, K., Moonmuang, S., Kitidee, K., Nangola, S., Sanghiran, L.V., Hong, S.S., Boulanger, P., Tayapiwatana, C., Chen, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 16.95 kDa
Atom Count: 1,323
Modeled Residue Count: 154
Deposited Residue Count: 154
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Artificial ankyrin repeat protein_Ank(GAG)1D4 mutant -S45Y	A	154	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.210 (Depositor), 0.210 (DCC)
R-Value Work: 0.187 (Depositor), 0.190 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.828	α = 90
b = 29.313	β = 98.58
c = 51.291	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-06-28

Deposition Author(s):

Chuankhayan, P.

Wisitponchai, T.

Sanghiran, L.V.

Tayapiwatana, C.

Revision History (Full details and data files)

Version 1.0: 2017-06-28
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.