3W9T
pore-forming CEL-III
- PDB DOI: https://doi.org/10.2210/pdb3W9T/pdb
- Classification: TOXIN
- Organism(s): Cucumaria echinata
- Mutation(s): No 
- Deposited: 2013-04-16 Released: 2014-03-19 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.273 
- R-Value Work: 0.239 
- R-Value Observed: 0.241 
wwPDB Validation   3D Report Full Report
This is version 4.0 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 |
Hemolytic lectin CEL-III | 432 | Cucumaria echinata | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for Q868M7 (Cucumaria echinata) Explore Q868M7  Go to UniProtKB:  Q868M7 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q868M7 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-galactopyranose-(1-4)-beta-D-fructofuranose | AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, T, U, V, W, X, Y, Z | 2 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G57229GY GlyCosmos:  G57229GY |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CA Query on CA | AB [auth C] AC [auth F] BB [auth C] BC [auth F] CB [auth C] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
MG Query on MG | DC [auth F] EC [auth F] FB [auth C] GB [auth C] MC [auth E] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
PCA Query on PCA | A B [auth C] C [auth G] D [auth B] E [auth F] A, B [auth C], C [auth G], D [auth B], E [auth F], F [auth E], G [auth D] | L-PEPTIDE LINKING | C5 H7 N O3 | GLN |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900038 Query on PRD_900038 | AA [auth H] BA [auth I] CA [auth J] DA [auth K] EA [auth L] | lactulose | Oligosaccharide / Water retention |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.273 
- R-Value Work: 0.239 
- R-Value Observed: 0.241 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 219.8 | α = 90 |
b = 228.65 | β = 127.13 |
c = 133.02 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | model building |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHENIX | phasing |
Entry History 
Deposition Data
- Released Date: 2014-03-19  Deposition Author(s): Unno, H., Goda, S., Hatakeyama, T.
Revision History (Full details and data files)
- Version 1.0: 2014-03-19
Type: Initial release - Version 1.1: 2014-05-21
Changes: Other - Version 2.0: 2018-07-25
Changes: Advisory, Data collection, Database references, Non-polymer description, Source and taxonomy, Structure summary - Version 3.0: 2019-12-25
Changes: Derived calculations, Polymer sequence - Version 4.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary