3RJQ

Crystal structure of anti-HIV llama VHH antibody A12 in complex with C186 gp120

PDB DOI: https://doi.org/10.2210/pdb3RJQ/pdb

Classification: Viral Protein/Immune system
Organism(s): HIV-1 M:B_HXB2R, Lama glama
Mutation(s): No

Deposited: 2011-04-15 Released: 2012-05-02
Deposition Author(s): Chen, L., McLellan, J.S., Kwon, Y.D., Schmidt, S., Wu, X., Zhou, T., Yang, Y., Zhang, B., Forsman, A., Weiss, R.A., Verrips, T., Mascola, J., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.299 (Depositor), 0.295 (DCC)
R-Value Work:
0.255 (Depositor), 0.262 (DCC)
R-Value Observed:
0.257 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of anti-HIV A12 VHH of llama antibody in complex with C1086 gp120

Chen, L., McLellan, J.S., Kwon, Y.D., Schmidt, S., Wu, X., Zhou, T., Yang, Y., Zhang, B., Forsman, A., Weiss, R.A., Verrips, T., Mascola, J., Kwong, P.D.

To be published.

Macromolecule Content

Total Structure Weight: 59.98 kDa
Atom Count: 3,390
Modelled Residue Count: 419
Deposited Residue Count: 525
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C186 gp120	A	382	HIV-1 M:B_HXB2R	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Llama VHH A12	B	143	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] 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] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] 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] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] 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] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.299 (Depositor), 0.295 (DCC)
R-Value Work: 0.255 (Depositor), 0.262 (DCC)
R-Value Observed: 0.257 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.6	α = 90
b = 66.6	β = 90
c = 266.92	γ = 90

Software Package:

Software Name	Purpose
SERGUI	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: 2012-05-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-05-02
Type: Initial release
Version 1.1: 2012-06-13
Changes: Database references
Version 1.2: 2012-09-12
Changes: Structure summary
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 1.4: 2024-10-30
Changes: Advisory, Data collection, Database references, Structure summary