4U36
Crystal structure of a seed lectin from Vatairea macrocarpa complexed with Tn-antigen
- PDB DOI: https://doi.org/10.2210/pdb4U36/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Vatairea macrocarpa
- Mutation(s): No
- Deposited: 2014-07-18 Released: 2014-12-31
- Funding Organization(s): Brazilian National Council for Scientific and Technological Development (CNPq), CAPES
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.197
- R-Value Work: 0.178
- R-Value Observed: 0.179
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 |
| Seed lectin | 240 | Vatairea macrocarpa | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P81371 (Vatairea macrocarpa) Explore P81371 Go to UniProtKB: P81371 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P81371 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| A2G Query on A2G | J [auth A] | 2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N |  | ||
| CIT Query on CIT | H [auth A] | CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N |  | ||
| SER Query on SER | I [auth A] | SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N |  | ||
| SO4 Query on SO4 | D [auth A], E [auth A], F [auth A], G [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| MN Query on MN | B [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| CA Query on CA | C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.197
- R-Value Work: 0.178
- R-Value Observed: 0.179
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 56.076 | α = 90 |
| b = 85.808 | β = 90 |
| c = 129.057 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2014-12-31 Deposition Author(s): Sousa, B.L., Silva-Filho, J.C., Kumar, P., Lyskowski, A., Bezerra, G.A., Delatorre, P., Rocha, B.A.M., Nagano, C.S., Gruber, K., Cavada, B.S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Brazilian National Council for Scientific and Technological Development (CNPq) | Brazil | -- |
| CAPES | Brazil | -- |
Revision History (Full details and data files)
- Version 1.0: 2014-12-31
Type: Initial release - Version 1.1: 2015-01-21
Changes: Database references - Version 1.2: 2017-08-23
Changes: Data collection, Derived calculations, Source and taxonomy - Version 1.3: 2019-04-17
Changes: Author supporting evidence, Data collection - Version 1.4: 2020-01-08
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary
