Download MendeleyCrystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219
Arai, R., Komatsu, M., Dong, J., Ueda, H.To be published.
5X5X
Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219
- PDB DOI: https://doi.org/10.2210/pdb5X5X/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2017-02-18 Released: 2018-02-21
- Funding Organization(s): Cooperative Research Program of Network Joint Research Center for Materials and Devices, Japan Society for the Promotion of Science
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.224
- R-Value Work: 0.181
- R-Value Observed: 0.183
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Fd chain of anti-osteocalcin antibody KTM219 | A [auth H] | 249 | Mus musculus | 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 |
| L chain of anti-osteocalcin antibody KTM219 | B [auth L] | 232 | 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 | |
| PG4 Query on PG4 | G [auth H], H | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| PGE Query on PGE | K [auth L], L | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | ||
| PEG Query on PEG | C [auth H], D [auth H], E [auth H], F [auth H] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| FMT Query on FMT | I [auth H], J [auth H], M [auth L] | FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.224
- R-Value Work: 0.181
- R-Value Observed: 0.183
- Space Group: P 21 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 64.8 | α = 90 |
| b = 71.472 | β = 90 |
| c = 96.882 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
| Coot | model building |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SCALEPACK | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-02-21 Deposition Author(s): Komatsu, M., Dong, J., Ueda, H., Arai, R.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Cooperative Research Program of Network Joint Research Center for Materials and Devices | Japan | 20161175 |
| Japan Society for the Promotion of Science | Japan | JP15H04191 |
| Japan Society for the Promotion of Science | Japan | JP24780097 |
| Japan Society for the Promotion of Science | Japan | JP16H00761 |
| Japan Society for the Promotion of Science | Japan | JP16K05841 |
| Japan Society for the Promotion of Science | Japan | JP26420793 |
| Japan Society for the Promotion of Science | Japan | JP24360336 |
Revision History (Full details and data files)
- Version 1.0: 2018-02-21
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
