2O40

Crystal Structure of a Chemically Synthesized 203 Amino Acid 'Covalent Dimer' HIV-1 Protease Molecule

PDB DOI: https://doi.org/10.2210/pdb2O40/pdb

Classification: Hydrolase/Hydrolase inhibitor
Organism(s): Human immunodeficiency virus 1
Mutation(s): No

Deposited: 2006-12-02 Released: 2006-12-19
Deposition Author(s): Torbeev, V.Y., Kent, S.B.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.237
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Convergent chemical synthesis and crystal structure of a 203 amino acid "covalent dimer" HIV-1 protease enzyme molecule.

Torbeev, V.Y., Kent, S.B.

(2007) Angew Chem Int Ed Engl 46: 1667-1670

PubMed: 17397076 Search on PubMed
DOI: https://doi.org/10.1002/anie.200604087
Primary Citation of Related Structures:
2O40

Organizational Affiliation

Department of Chemistry, Institute for Biophysical Dynamics, Gordon Center for Integrative Science, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.

Macromolecule Content

Total Structure Weight: 22.66 kDa
Atom Count: 1,654
Modelled Residue Count: 203
Deposited Residue Count: 203
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
covalent dimer HIV-1 protease	A	203	N/A	Mutation(s): 0 EC: 3.4.23.16
UniProt
Find proteins for O38716 (Human immunodeficiency virus 1) Explore O38716 Go to UniProtKB: O38716
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O38716
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2NC Query on 2NC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide C₃₅ H₆₈ N₁₁ O₈ MQPXOVRKKPPKFZ-QYKDHROSSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA Query on ABA	A	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
NLE Query on NLE	A	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU
YCM Query on YCM	A	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₃ S		CYS

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000398 (2NC) Query on PRD_000398	B [auth A]	N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide	Peptide-like / Inhibitor		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.237
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.326	α = 90
b = 58.306	β = 90
c = 61.699	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-12-19

Deposition Author(s):

Torbeev, V.Y.

Kent, S.B.H.

Revision History (Full details and data files)

Version 1.0: 2006-12-19
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.3: 2013-02-27
Changes: Other
Version 1.4: 2017-10-18
Changes: Refinement description
Version 1.5: 2023-12-27
Changes: Data collection, Database references, Derived calculations