1NC2
Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Y-DOTA
- PDB DOI: https://doi.org/10.2210/pdb1NC2/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Mutation(s): No
- Deposited: 2002-12-04 Released: 2003-12-16
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.247
- R-Value Work: 0.209
- R-Value Observed: 0.209
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 |
| MONOCLONAL ANTIBODY 2D12.5, LAMBDA LIGHT CHAIN | 215 | 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 |
| MONOCLONAL ANTIBODY 2D12.5, IGG1 GAMMA HEAVY CHAIN | 221 | 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: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| MONOCLONAL ANTIBODY 2D12.5, IGG1 GAMMA HEAVY CHAIN | 221 | 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 | |
| DOE Query on DOE | G [auth B], K [auth D] | (S)-2-(4-(2-(2-HYDROXYETHYLTHIO)-ACETAMIDO)-BENZYL)-1,4,7,10-TETRAAZACYCLODODECANE-N,N',N'',N'''-TETRAACETATE C27 H41 N5 O10 S PMSNEOWGSKSXKR-QFIPXVFZSA-N |  | ||
| NAG Query on NAG | I [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| YT3 Query on YT3 | F [auth B], J [auth D] | YTTRIUM (III) ION Y GRTBAGCGDOYUBE-UHFFFAOYSA-N |  | ||
| CL Query on CL | E [auth A], H [auth C] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| PCA Query on PCA | B | L-PEPTIDE LINKING | C5 H7 N O3 |  | GLN |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.247
- R-Value Work: 0.209
- R-Value Observed: 0.209
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 67.335 | α = 90 |
| b = 81.3 | β = 90 |
| c = 160.923 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| AMoRE | phasing |
| CNS | refinement |
Entry History
Deposition Data
- Released Date: 2003-12-16 Deposition Author(s): Corneillie, T.M., Fisher, A.J., Meares, C.F.
Revision History (Full details and data files)
- Version 1.0: 2003-12-16
Type: Initial release - Version 1.1: 2008-04-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 2.0: 2019-12-25
Changes: Derived calculations, Polymer sequence - Version 2.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 2.2: 2023-08-16
Changes: Data collection, Database references, Refinement description, Structure summary
