3U4E

Crystal Structure of PG9 Fab in Complex with V1V2 Region from HIV-1 strain CAP45

PDB DOI: https://doi.org/10.2210/pdb3U4E/pdb

Classification: IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2011-10-07 Released: 2011-11-30
Deposition Author(s): Gorman, J., McLellan, J., Pancera, M., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.234
R-Value Work: 0.182
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

This is version 3.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 132.97 kDa
Atom Count: 9,320
Modelled Residue Count: 1,112
Deposited Residue Count: 1,176
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V1V2 region of HIV-1 on 1FD6 scaffold	A [auth G], B [auth J]	124	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q1PHM9 (Human immunodeficiency virus 1) Explore Q1PHM9 Go to UniProtKB: Q1PHM9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1PHM9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PG9 Heavy Chain	C [auth H], E [auth A]	248	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PG9 Light Chain	D [auth L], F [auth B]	216	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth C], I [auth E]	7		N-Glycosylation	Interactions Focus chain G [auth C] Focus chain I [auth E] Interactions & Density Focus chain G [auth C] Focus chain I [auth E]
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth D]	6		N-Glycosylation	Interactions Focus chain H [auth D] Interactions & Density Focus chain H [auth D]
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth F]	2		N-Glycosylation	Interactions Focus chain J [auth F] Interactions & Density Focus chain J [auth F]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose	K [auth I]	2		N/A	Interactions Focus chain K [auth I] Interactions & Density Focus chain K [auth I]
Glycosylation Resources
GlyTouCan: G07696MJ GlyCosmos: G07696MJ GlyGen: G07696MJ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L [auth G] SDF format, chain M [auth L] SDF format, chain N [auth L] SDF format, chain O [auth L] SDF format, chain P [auth L] SDF format, chain Q [auth L] SDF format, chain R [auth L] SDF format, chain S [auth L] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain L [auth G] MOL2 format, chain M [auth L] MOL2 format, chain N [auth L] MOL2 format, chain O [auth L] MOL2 format, chain P [auth L] MOL2 format, chain Q [auth L] MOL2 format, chain R [auth L] MOL2 format, chain S [auth L] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	L [auth G] M [auth L] N [auth L] O [auth L] P [auth L] L [auth G], M [auth L], N [auth L], O [auth L], P [auth L], Q [auth L], R [auth L], S [auth L], T [auth B], U [auth B], V [auth B], W [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth G] Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth L] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain L [auth G] Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth L] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	C [auth H], E [auth A]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN
TYS Query on TYS	C [auth H], E [auth A]	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.234
R-Value Work: 0.182
R-Value Observed: 0.184
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.026	α = 90
b = 103.545	β = 90
c = 186.373	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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Entry History

Deposition Data

Released Date: 2011-11-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-30
Type: Initial release
Version 1.1: 2011-12-21
Changes: Database references
Version 2.0: 2019-12-25
Changes: Advisory, Derived calculations, Polymer sequence
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 3.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 3.2: 2023-12-06
Changes: Data collection