5BZD | pdb_00005bzd

Crystal Structure of PCDN-27A, an antibody from the PCDN family of HIV-1 antibodies

PDB DOI: https://doi.org/10.2210/pdb5BZD/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2015-06-11 Released: 2016-05-25
Deposition Author(s): Garces, F., WILSON, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.247 (Depositor), 0.245 (DCC)
R-Value Work:
0.211 (Depositor), 0.212 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Early Antibody Lineage Diversification and Independent Limb Maturation Lead to Broad HIV-1 Neutralization Targeting the Env High-Mannose Patch

MacLead, D., Choi, N.M., Briney, B., Garces, F., Ver, L.S., Landais, E., Murrell, B., Wrin, T., Kilembe, W., Liang, C.-H., Ramos, A., Bian, C., Wickramasinghe, L., Kong, L., Eren, K., Wu, C.-Y., Wong, C.-H., The IAVI Protocol C Investigators & The IAVI African HIV Research Network, Pond, S.L.K., Wilson, I.A., Burton, D.R., Poignard, P.

(2016) Immunity 44: 1215-1226

Macromolecule Content

Total Structure Weight: 96.58 kDa
Atom Count: 6,733
Modeled Residue Count: 882
Deposited Residue Count: 892
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5G8 HIV Antibody light chain	A, C	214	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5G8 HIV Antibody heavy chain	B, D	232	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.247 (Depositor), 0.245 (DCC)
R-Value Work: 0.211 (Depositor), 0.212 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.861	α = 90
b = 120.375	β = 96.43
c = 111.098	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-05-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-05-25
Type: Initial release
Version 1.1: 2016-07-27
Changes: Data collection
Version 1.2: 2017-09-27
Changes: Author supporting evidence, Derived calculations
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.