4YAQ
Crystal structure of a computationally optimized PG9 mutant
- PDB DOI: https://doi.org/10.2210/pdb4YAQ/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2015-02-17 Released: 2015-06-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.238
- R-Value Work: 0.204
- R-Value Observed: 0.206
wwPDB Validation 3D Report Full Report
This is version 2.2 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 |
| PG9_N100FY Fab heavy chain | A [auth H], C [auth A] | 248 | Homo sapiens | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| PG9_N100FY Light Chain | B [auth L], D [auth B] | 216 | Homo sapiens | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for Q6GMW3 (Homo sapiens) Explore Q6GMW3 Go to UniProtKB: Q6GMW3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6GMW3 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | E [auth C], F [auth D] | 3 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB | |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MES Query on MES | G [auth H], I [auth L], J [auth L], L [auth B] | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N |  | ||
| PO4 Query on PO4 | H, K [auth L] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| Modified Residues 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| PCA Query on PCA | A [auth H], C [auth A] | L-PEPTIDE LINKING | C5 H7 N O3 |  | GLN |
| TYS Query on TYS | A [auth H], C [auth A] | L-PEPTIDE LINKING | C9 H11 N O6 S |  | TYR |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.238
- R-Value Work: 0.204
- R-Value Observed: 0.206
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 57.74 | α = 90 |
| b = 122.98 | β = 96.27 |
| c = 69.92 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2015-06-03 Deposition Author(s): Murrell, S., Julien, J.P., Wilson, I.A.
Revision History (Full details and data files)
- Version 1.0: 2015-06-03
Type: Initial release - Version 1.1: 2015-06-10
Changes: Database references - Version 1.2: 2017-08-23
Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Polymer sequence, Structure summary - Version 2.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary - Version 2.2: 2023-11-15
Changes: Data collection
