4JZW

Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in P212121 space group

PDB DOI: https://doi.org/10.2210/pdb4JZW/pdb

Classification: Viral protein/INHIBITOR
Organism(s): Human immunodeficiency virus 1
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2013-04-03 Released: 2013-06-12
Deposition Author(s): Acharya, P., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.209
R-Value Work: 0.164
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 94.22 kDa
Atom Count: 7,061
Modelled Residue Count: 731
Deposited Residue Count: 808
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 YU2 gp120 glycoprotein	A, B [auth G]	376	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: gp120
UniProt
Find proteins for P35961 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2)) Explore P35961 Go to UniProtKB: P35961
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35961
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CD4-MIMETIC MINIPROTEIN M48U1	C [auth M], D [auth R]	28	N/A	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain R [auth A] SDF format, chain U [auth G] SDF format, chain V [auth G] SDF format, chain W [auth G] SDF format, chain X [auth G] SDF format, chain Z [auth G] SDF format, chain BA [auth G] SDF format, chain Y [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain R [auth A] MOL2 format, chain U [auth G] MOL2 format, chain V [auth G] MOL2 format, chain W [auth G] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain Y [auth G]	AA [auth G] BA [auth G] E [auth A] F [auth A] G [auth A] AA [auth G], BA [auth G], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], R [auth A], U [auth G], V [auth G], W [auth G], X [auth G], Y [auth G], Z [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth A] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth A] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain GA [auth G] SDF format, chain Q [auth A] MOL2 format, chain GA [auth G] MOL2 format, chain Q [auth A]	GA [auth G], Q [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain GA [auth G] Focus chain Q [auth A] Interactions & Density Focus chain GA [auth G] Focus chain Q [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain FA [auth G] MOL2 format, chain FA [auth G]	FA [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FA [auth G] Interactions & Density Focus chain FA [auth G]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain DA [auth G] SDF format, chain EA [auth G] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A]	CA [auth G] DA [auth G] EA [auth G] N [auth A] O [auth A] CA [auth G], DA [auth G], EA [auth G], N [auth A], O [auth A], P [auth A], S [auth A], T [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth A] Focus chain T [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
U2X Query on U2X	C [auth M], D [auth R]	L-PEPTIDE LINKING	C₁₆ H₂₃ N O₃		TYR

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001094 Query on PRD_001094	C [auth M], D [auth R]	CD4-MIMETIC MINIPROTEIN M48U1	Peptide-like / Inhibitor		Interactions Focus chain C [auth M] Focus chain D [auth R] Interactions & Density Focus chain C [auth M] Focus chain D [auth R]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.209
R-Value Work: 0.164
R-Value Observed: 0.166
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.651	α = 90
b = 78.009	β = 90
c = 163.25	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-06-12

Deposition Author(s):

Acharya, P.

Kwong, P.D.

Revision History (Full details and data files)

Version 1.0: 2013-06-12
Type: Initial release
Version 1.1: 2013-07-10
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary