4LAJ

Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex with CD4-mimetic miniprotein, M48U1, and llama single-domain, broadly neutralizing, co-receptor binding site antibody, JM4

PDB DOI: https://doi.org/10.2210/pdb4LAJ/pdb

Classification: VIRAL PROTEIN/INHIBITOR
Organism(s): Human immunodeficiency virus 1, Lama glama
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2013-06-20 Released: 2013-08-14
Deposition Author(s): Acharya, P., Luongo, T.S., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.227
R-Value Work: 0.185
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 243.36 kDa
Atom Count: 16,384
Modelled Residue Count: 1,962
Deposited Residue Count: 2,132
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 YU2 gp120 envelope glycoprotein	A [auth J], B [auth F], C [auth A], D [auth B]	376	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: Env
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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CD4-mimetic miniprotein M48U1	E [auth K], F [auth D], G, H [auth C]	28	N/A	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Llama single domain antibody, JM4	I [auth H], J [auth M], K [auth L], L [auth I]	129	Lama glama	Mutation(s): 0
UniProt
Find proteins for A2KD57 (Lama glama) Explore A2KD57 Go to UniProtKB: A2KD57
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2KD57
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 F] SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain M [auth J] SDF format, chain MA [auth A] SDF format, chain N [auth J] SDF format, chain NA [auth A] SDF format, chain O [auth J] SDF format, chain P [auth J] SDF format, chain Q [auth J] SDF format, chain R [auth J] SDF format, chain RA [auth B] SDF format, chain S [auth J] SDF format, chain SA [auth B] SDF format, chain T [auth J] SDF format, chain TA [auth B] SDF format, chain U [auth J] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain W [auth F] SDF format, chain WA [auth B] SDF format, chain X [auth F] SDF format, chain XA [auth B] SDF format, chain Y [auth F] SDF format, chain YA [auth B] SDF format, chain Z [auth F] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain M [auth J] MOL2 format, chain MA [auth A] MOL2 format, chain N [auth J] MOL2 format, chain NA [auth A] MOL2 format, chain O [auth J] MOL2 format, chain P [auth J] MOL2 format, chain Q [auth J] MOL2 format, chain R [auth J] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth J] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth J] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth J] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth F] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth F] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth F] MOL2 format, chain YA [auth B] MOL2 format, chain Z [auth F]	AA [auth F] BA [auth F] CA [auth F] DA [auth F] EA [auth F] AA [auth F], BA [auth F], CA [auth F], DA [auth F], EA [auth F], FA [auth A], GA [auth A], HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A], M [auth J], MA [auth A], N [auth J], NA [auth A], O [auth J], P [auth J], Q [auth J], R [auth J], RA [auth B], S [auth J], SA [auth B], T [auth J], TA [auth B], U [auth J], UA [auth B], VA [auth B], W [auth F], WA [auth B], X [auth F], XA [auth B], Y [auth F], YA [auth B], Z [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain M [auth J] Focus chain MA [auth A] Focus chain N [auth J] Focus chain NA [auth A] Focus chain O [auth J] Focus chain P [auth J] Focus chain Q [auth J] Focus chain R [auth J] Focus chain RA [auth B] Focus chain S [auth J] Focus chain SA [auth B] Focus chain T [auth J] Focus chain TA [auth B] Focus chain U [auth J] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain W [auth F] Focus chain WA [auth B] Focus chain X [auth F] Focus chain XA [auth B] Focus chain Y [auth F] Focus chain YA [auth B] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain M [auth J] Focus chain MA [auth A] Focus chain N [auth J] Focus chain NA [auth A] Focus chain O [auth J] Focus chain P [auth J] Focus chain Q [auth J] Focus chain R [auth J] Focus chain RA [auth B] Focus chain S [auth J] Focus chain SA [auth B] Focus chain T [auth J] Focus chain TA [auth B] Focus chain U [auth J] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain W [auth F] Focus chain WA [auth B] Focus chain X [auth F] Focus chain XA [auth B] Focus chain Y [auth F] Focus chain YA [auth B] Focus chain Z [auth F]
ACA Query on ACA Download Ideal Coordinates CCD File SDF format, chain CB [auth B] MOL2 format, chain CB [auth B]	CB [auth B]	6-AMINOHEXANOIC ACID C₆ H₁₃ N O₂ SLXKOJJOQWFEFD-UHFFFAOYSA-N		Interactions Focus chain CB [auth B] Interactions & Density Focus chain CB [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain BB [auth B] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain V [auth J] SDF format, chain ZA [auth B] MOL2 format, chain AB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain V [auth J] MOL2 format, chain ZA [auth B]	AB [auth B] BB [auth B] OA [auth A] PA [auth A] QA [auth A] AB [auth B], BB [auth B], OA [auth A], PA [auth A], QA [auth A], V [auth J], ZA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain BB [auth B] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain V [auth J] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth B] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain V [auth J] Focus chain ZA [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
U2X Query on U2X	E [auth K], F [auth D], G, H [auth C]	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	E [auth C], F [auth D], G, H [auth K]	CD4-MIMETIC MINIPROTEIN M48U1	Peptide-like / Inhibitor		Interactions Focus chain E [auth K] Focus chain F [auth D] Focus chain G Focus chain H [auth C] Interactions & Density Focus chain E [auth K] Focus chain F [auth D] Focus chain G Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.227
R-Value Work: 0.185
R-Value Observed: 0.188
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.772	α = 90
b = 86.221	β = 102.88
c = 144.848	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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-08-14

Deposition Author(s):

Acharya, P.

Luongo, T.S.

Kwong, P.D.

Revision History (Full details and data files)

Version 1.0: 2013-08-14
Type: Initial release
Version 1.1: 2013-08-21
Changes: Structure summary
Version 1.2: 2013-09-04
Changes: Database references
Version 1.3: 2014-04-09
Changes: Source and taxonomy
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection