6C5H
S25-5 Fab in complex with Chlamydiaceae-specific LPS antigen
- PDB DOI: https://doi.org/10.2210/pdb6C5H/pdb
- Classification: IMMUNE SYSTEM, SUGAR BINDING PROTEIN
- Organism(s): Mus musculus
- Mutation(s): No
- Deposited: 2018-01-16 Released: 2019-01-09
- Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.99 Å
- R-Value Free: 0.226
- R-Value Work: 0.187
- R-Value Observed: 0.189
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 |
| Fab Heavy Chain (IgG1) | A [auth H] | 218 | Mus musculus | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for Q99LC4 (Mus musculus) Explore Q99LC4 Go to UniProtKB: Q99LC4 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q99LC4 | ||||
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 |
| Fab Light Chain (IgG1 Kappa) | B [auth L] | 219 | Mus musculus | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for A0A0F7R5U8 (Mus musculus) Explore A0A0F7R5U8 Go to UniProtKB: A0A0F7R5U8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A0F7R5U8 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | C [auth A] | 2 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC | |||||
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-8)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose | D [auth B] | 5 |  | N/A | |
Glycosylation Resources | |||||
GlyTouCan: G21745XJ GlyCosmos: G21745XJ | |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PG4 Query on PG4 | E [auth H] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| TAM Query on TAM | H | TRIS(HYDROXYETHYL)AMINOMETHANE C7 H17 N O3 GKODZWOPPOTFGA-UHFFFAOYSA-N |  | ||
| PEG Query on PEG | F [auth H], G [auth H] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| CL Query on CL | I [auth L] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| PCA Query on PCA | A [auth H] | L-PEPTIDE LINKING | C5 H7 N O3 |  | GLN |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.99 Å
- R-Value Free: 0.226
- R-Value Work: 0.187
- R-Value Observed: 0.189
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 52.146 | α = 90 |
| b = 128.957 | β = 90 |
| c = 135.428 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| SCALEPACK | data scaling |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-01-09 Deposition Author(s): Evans, S.V., Haji-Ghassemi, O.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Natural Sciences and Engineering Research Council (NSERC, Canada) | Canada | Discovery Grant 171356-2013 |
Revision History (Full details and data files)
- Version 1.0: 2019-01-09
Type: Initial release - Version 1.1: 2019-02-27
Changes: Data collection, Database references - Version 2.0: 2020-01-08
Changes: Author supporting evidence, Data collection, 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: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
