5LGH
Afamin antibody fragment, N14 Fab, L1- glycosilated, crystal form II, same as 5L7X, but isomorphous setting indexed same as 5L88, 5L9D
- PDB DOI: https://doi.org/10.2210/pdb5LGH/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Mutation(s): No
- Deposited: 2016-07-07 Released: 2016-08-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.86 Å
- R-Value Free: 0.228
- R-Value Work: 0.190
- R-Value Observed: 0.192
This is version 1.4 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 |
| MOUSE ANTIBODY FAB FRAGMENT, IGG1-KAPPA HEAVY CHAIN | A [auth H] | 220 | Mus musculus | 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: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| MOUSE ANTIBODY FAB FRAGMENT, IGG1-KAPPA LIGHT CHAIN | B [auth L] | 215 | Mus musculus | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 1PE Query on 1PE | G [auth L] | PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N |  | ||
| NAG Query on NAG | H [auth L] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| PG4 Query on PG4 | C [auth H] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| PEG Query on PEG | D [auth H], E [auth H], F [auth H] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.86 Å
- R-Value Free: 0.228
- R-Value Work: 0.190
- R-Value Observed: 0.192
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.196 | α = 90 |
| b = 67.491 | β = 90 |
| c = 88.941 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| autoPROC | data reduction |
| XSCALE | data scaling |
| Aimless | data scaling |
| BALBES | phasing |
Entry History
Deposition Data
- Released Date: 2016-08-03 Deposition Author(s): Rupp, B., Naschberger, A.
Revision History (Full details and data files)
- Version 1.0: 2016-08-03
Type: Initial release - Version 1.1: 2016-12-07
Changes: Database references - Version 1.2: 2016-12-21
Changes: Database references - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Refinement description, Structure summary - Version 1.4: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
