6CBJ
Crystal Structure of DH270.3 Fab in complex with Man9
- PDB DOI: https://doi.org/10.2210/pdb6CBJ/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2018-02-03 Released: 2018-02-21 
- Funding Organization(s): amfAR, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.85 Å
- R-Value Free: 0.231 
- R-Value Work: 0.204 
- R-Value Observed: 0.205 
wwPDB Validation   3D Report Full Report
This is version 2.1 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 |
DH270.3 Fab heavy chain | A [auth H] | 238 | Homo sapiens | Mutation(s): 0  | |
UniProt | |||||
Find proteins for S6C4S0 (Homo sapiens) Explore S6C4S0  Go to UniProtKB:  S6C4S0 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | S6C4S0 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
DH270.3 Fab light chain | B [auth L] | 216 | Homo sapiens | Mutation(s): 0  | |
UniProt | |||||
Find proteins for Q6PJG0 (Homo sapiens) Explore Q6PJG0  Go to UniProtKB:  Q6PJG0 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q6PJG0 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C [auth A] | 11 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G60230HH GlyCosmos:  G60230HH GlyGen:  G60230HH |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
PO4 Query on PO4 | D [auth H] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.85 Å
- R-Value Free: 0.231 
- R-Value Work: 0.204 
- R-Value Observed: 0.205 
- Space Group: I 41
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 128.087 | α = 90 |
b = 128.087 | β = 90 |
c = 91.875 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
Coot | model building |
XDS | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-02-21  Deposition Author(s): Fera, D., Harrison, S.C.
Funding Organization | Location | Grant Number |
---|---|---|
amfAR | United States | 109502-61-RKVA |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | 1F32-AI-116355 |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI100645 |
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | T32GM007171 |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | F30-AI122982 |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI127193 |
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | P41 GM103403 |
Revision History (Full details and data files)
- Version 1.0: 2018-02-21
Type: Initial release - Version 1.1: 2018-02-28
Changes: Author supporting evidence - Version 1.2: 2018-03-28
Changes: Data collection, Database references - Version 1.3: 2018-04-04
Changes: Data collection, Database references - Version 1.4: 2019-04-17
Changes: Author supporting evidence, Data collection, Database references - Version 1.5: 2019-12-18
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary