6W6T

WT HIV-1 Protease in Complex with Phosphonated UMass6 (PU6)

PDB DOI: https://doi.org/10.2210/pdb6W6T/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-03-17 Released: 2021-03-17
Deposition Author(s): Lockbaum, G.J., Henes, M., Kosovrasti, K., Nalivaika, E.A., Ali, A., KurtYilmaz, N., Schiffer, C.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.228
R-Value Work: 0.200
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

To Be Determined

Lockbaum, G.J., Henes, M., Kosovrasti, K., Nalivaika, E.A., Ali, A., KurtYilmaz, N., Schiffer, C.A.

To be published.

Macromolecule Content

Total Structure Weight: 22.69 kDa
Atom Count: 1,720
Modelled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A [auth B], B [auth A]	99	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497 Go to UniProtKB: P12497
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12497
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TK7 (Subject of Investigation/LOI) Query on TK7 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	diethyl [(4-{(2S,3R)-4-{[(4-aminophenyl)sulfonyl](2-ethylbutyl)amino}-2-[({[(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl]oxy}carbonyl)amino]-3-hydroxybutyl}phenoxy)methyl]phosphonate C₃₄ H₅₂ N₃ O₁₁ P S BEYLPLHLWVCWJA-NKVOBILMSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	C [auth B], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.228
R-Value Work: 0.200
R-Value Observed: 0.201
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.13	α = 90
b = 57.953	β = 90
c = 61.694	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building
HKL-3000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-03-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P01-GM109767

Revision History (Full details and data files)

Version 1.0: 2021-03-17
Type: Initial release
Version 2.0: 2023-10-18
Changes: Data collection, Database references, Non-polymer description, Refinement description

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Deposit Data

Help and Resources

6W6T

WT HIV-1 Protease in Complex with Phosphonated UMass6 (PU6)

To Be Determined

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)