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 
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. 
Macromolecules
Find similar proteins by:
(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 AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
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 AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
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 AnnotationsExpand | |||||
|
Oligosaccharides
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 | ||
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 | ||
Glycosylation Resources | |||||
GlyTouCan:  G09724ZC GlyCosmos:  G09724ZC GlyGen:  G09724ZC |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SO4 Query on SO4 | L [auth G] M [auth L] N [auth L] O [auth L] P [auth L] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
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 Name | Purpose |
---|---|
SERGUI | data collection |
PHASER | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2011-11-30  Deposition Author(s): Gorman, J., McLellan, J., Pancera, M., Kwong, P.D.
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