3LL2
Monomeric Griffithsin in Complex with a High-Mannose Branched Carbohydrate
- PDB DOI: https://doi.org/10.2210/pdb3LL2/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Griffithsia sp. Q66D336
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2010-01-28 Released: 2010-10-06
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 0.97 Å
- R-Value Free: 0.155
- R-Value Work: 0.143
- R-Value Observed: 0.144
wwPDB Validation 3D Report Full Report
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 |
| Griffithsin | 123 | Griffithsia sp. Q66D336 | Mutation(s): 1 |  | |
UniProt | |||||
Find proteins for P84801 (Griffithsia sp. (strain Q66D336)) Explore P84801 Go to UniProtKB: P84801 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P84801 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| 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-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose | B | 8 |  | N/A | |
Glycosylation Resources | |||||
GlyTouCan: G04869AE GlyCosmos: G04869AE | |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PEG Query on PEG | I [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 0.97 Å
- R-Value Free: 0.155
- R-Value Work: 0.143
- R-Value Observed: 0.144
- Space Group: I 41
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 90.5 | α = 90 |
| b = 90.5 | β = 90 |
| c = 27.8 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
Entry History
Deposition Data
- Released Date: 2010-10-06 Deposition Author(s): Moulaei, T., Wlodawer, A.
Revision History (Full details and data files)
- Version 1.0: 2010-10-06
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2021-10-13
Changes: Database references, Structure summary - Version 2.2: 2023-09-06
Changes: Data collection, Refinement description
