3OKD
Crystal structure of S25-39 in complex with Kdo
- PDB DOI: https://doi.org/10.2210/pdb3OKD/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Mutation(s): No 
- Deposited: 2010-08-24 Released: 2011-04-06 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.275 
- R-Value Work: 0.233 
- R-Value Observed: 0.235 
This is version 1.3 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 |
S25-39 Fab (IgG1k) light chain | 219 | 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 |
S25-39 Fab (IgG1k) heavy chain | 222 | Mus musculus | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
KDO Query on KDO | E [auth B] | 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid C8 H14 O8 NNLZBVFSCVTSLA-HXUQBWEZSA-N | |||
PEG Query on PEG | C [auth A], D [auth B] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N | |||
ZN Query on ZN | F [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.275 
- R-Value Work: 0.233 
- R-Value Observed: 0.235 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 45.747 | α = 90 |
b = 82.011 | β = 90 |
c = 131.976 | γ = 90 |
Software Name | Purpose |
---|---|
d*TREK | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
Entry History 
Deposition Data
- Released Date: 2011-04-06  Deposition Author(s): Blackler, R.J., Evans, S.V.
Revision History (Full details and data files)
- Version 1.0: 2011-04-06
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2018-03-07
Changes: Advisory, Data collection - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary