3TV3
Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with Man9
- PDB DOI: https://doi.org/10.2210/pdb3TV3/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2011-09-19 Released: 2011-10-19
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.29 Å
- R-Value Free: 0.184
- R-Value Work: 0.159
- R-Value Observed: 0.159
wwPDB Validation 3D Report Full Report
This is version 3.1 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 |
| PGT128 light chain, Ig lambda-2 chain C regions | A [auth L] | 211 | Homo sapiens | Mutation(s): 0 Gene Names: IGLC2 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| PGT128 heavy chain, Ig gamma-1 chain C region | B [auth H] | 239 | Homo sapiens | Mutation(s): 0 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01857 (Homo sapiens) Explore P01857 Go to UniProtKB: P01857 | |||||
PHAROS: P01857 GTEx: ENSG00000211896 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01857 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose | C [auth A] | 8 |  | N/A | |
Glycosylation Resources | |||||
GlyTouCan: G65997KL GlyCosmos: G65997KL | |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EPE Query on EPE | I [auth H] | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | D [auth L], F [auth H], G [auth H], H | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| AML Query on AML | E [auth H] | AMYLAMINE C5 H13 N DPBLXKKOBLCELK-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| PCA Query on PCA | B [auth H] | L-PEPTIDE LINKING | C5 H7 N O3 |  | GLN |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.29 Å
- R-Value Free: 0.184
- R-Value Work: 0.159
- R-Value Observed: 0.159
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.143 | α = 90 |
| b = 106.017 | β = 90 |
| c = 145.311 | γ = 90 |
| Software Name | Purpose |
|---|---|
| Blu-Ice | data collection |
| PHASER | phasing |
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
Entry History
Deposition Data
- Released Date: 2011-10-19 Deposition Author(s): Pejchal, R., Wilson, I.A.
Revision History (Full details and data files)
- Version 1.0: 2011-10-19
Type: Initial release - Version 1.1: 2011-10-26
Changes: Database references - Version 1.2: 2011-12-07
Changes: Database references - Version 1.3: 2017-08-02
Changes: Refinement description, Source and taxonomy - Version 2.0: 2019-12-25
Changes: Advisory, Database references, Derived calculations, Polymer sequence - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 3.1: 2021-04-28
Changes: Derived calculations, Source and taxonomy, Structure summary
