3OAU

Antibody 2G12 Recognizes Di-Mannose Equivalently in Domain- and Non-Domain-Exchanged Forms, but only binds the HIV-1 Glycan Shield if Domain-Exchanged

PDB DOI: https://doi.org/10.2210/pdb3OAU/pdb

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

Deposited: 2010-08-05 Released: 2011-01-12
Deposition Author(s): Doores, K.J., Fulton, Z., Huber, M., Wilson, I.A., Burton, D.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.243
R-Value Work: 0.212
R-Value Observed: 0.213

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 47.73 kDa
Atom Count: 3,514
Modelled Residue Count: 430
Deposited Residue Count: 437
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 2G12, heavy chain	A [auth H]	225	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 2G12, light chain	B [auth L]	212	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	C [auth A]	2		N/A	Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
Glycosylation Resources
GlyTouCan: G53402KW GlyCosmos: G53402KW GlyGen: G53402KW

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain E [auth H] MOL2 format, chain D [auth H] MOL2 format, chain E [auth H]	D [auth H], E [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth H] Focus chain E [auth H] Interactions & Density Focus chain D [auth H] Focus chain E [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth L] MOL2 format, chain F [auth L]	F [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth L] Interactions & Density Focus chain F [auth L]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900111 Query on PRD_900111	C [auth A]	2alpha-alpha-mannobiose	Oligosaccharide / Metabolism		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.243
R-Value Work: 0.212
R-Value Observed: 0.213
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.301	α = 92.91
b = 56.628	β = 105.05
c = 57.653	γ = 92.74

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
BUSTER	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-01-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-01-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary

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3OAU

Antibody 2G12 Recognizes Di-Mannose Equivalently in Domain- and Non-Domain-Exchanged Forms, but only binds the HIV-1 Glycan Shield if Domain-Exchanged

Entity ID: 1

Entity Groups

Sequence Annotations

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Entity ID: 2