4K6U
Crystal structure of Ad37 fiber knob in complex with trivalent sialic acid inhibitor ME0386
- PDB DOI: https://doi.org/10.2210/pdb4K6U/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Human adenovirus D37
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2013-04-16 Released: 2014-10-22
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.222
- R-Value Work: 0.177
- R-Value Observed: 0.178
This is version 1.6 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 |
| Fiber protein | 194 | Human adenovirus D37 | Mutation(s): 0 Gene Names: L5 |  | |
UniProt | |||||
Find proteins for Q64823 (Human adenovirus D37) Explore Q64823 Go to UniProtKB: Q64823 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q64823 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 1P4 Query on 1P4 | H [auth B] | 3,3',3''-[nitrilotris(methanediyl-1H-1,2,3-triazole-4,1-diyl)]tripropan-1-ol C18 H30 N10 O3 VAKXPQHQQNOUEZ-UHFFFAOYSA-N |  | ||
| SIA Query on SIA | E [auth A], G [auth B], J [auth C] | N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N |  | ||
| ZN Query on ZN | D [auth A], F [auth B], I [auth C] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | K [auth C] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.222
- R-Value Work: 0.177
- R-Value Observed: 0.178
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 60.86 | α = 90 |
| b = 69.91 | β = 94.62 |
| c = 74.07 | γ = 90 |
| Software Name | Purpose |
|---|---|
| RemDAq | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
Entry History
Deposition Data
- Released Date: 2014-10-22 Deposition Author(s): Stehle, T., Bauer, J.
Revision History (Full details and data files)
- Version 1.0: 2014-10-22
Type: Initial release - Version 1.1: 2015-07-29
Changes: Database references - Version 1.2: 2015-09-09
Changes: Database references - Version 1.3: 2017-11-15
Changes: Refinement description - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.5: 2024-02-28
Changes: Data collection, Database references, Structure summary - Version 1.6: 2024-04-03
Changes: Refinement description
