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
Deposition Author(s): Unno, H., Goda, S., Hatakeyama, T.

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.

Macromolecule Content

Total Structure Weight: 346.93 kDa
Atom Count: 24,175
Modelled Residue Count: 3,024
Deposited Residue Count: 3,024
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemolytic lectin CEL-III	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]	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 Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain JA [auth j] Focus chain K Focus chain KA [auth k] Focus chain L Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain JA [auth j] Focus chain K Focus chain KA [auth k] Focus chain L Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z
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 Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain AC [auth F] SDF format, chain BB [auth C] SDF format, chain BC [auth F] SDF format, chain CB [auth C] SDF format, chain CC [auth F] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FC [auth F] SDF format, chain GC [auth F] SDF format, chain HB [auth C] SDF format, chain HC [auth E] SDF format, chain IB [auth C] SDF format, chain IC [auth E] SDF format, chain JB [auth G] SDF format, chain JC [auth E] SDF format, chain KB [auth G] SDF format, chain KC [auth E] SDF format, chain LB [auth G] SDF format, chain LC [auth E] SDF format, chain MB [auth G] SDF format, chain NB [auth G] SDF format, chain OC [auth E] SDF format, chain PC [auth E] SDF format, chain QB [auth G] SDF format, chain QC [auth D] SDF format, chain RB [auth B] SDF format, chain RC [auth D] SDF format, chain SA [auth A] SDF format, chain SB [auth B] SDF format, chain SC [auth D] SDF format, chain TA [auth A] SDF format, chain TB [auth B] SDF format, chain TC [auth D] SDF format, chain UA [auth A] SDF format, chain UB [auth B] SDF format, chain UC [auth D] SDF format, chain VA [auth A] SDF format, chain VB [auth B] SDF format, chain WA [auth A] SDF format, chain XC [auth D] SDF format, chain YB [auth B] SDF format, chain ZA [auth A] SDF format, chain ZB [auth F] MOL2 format, chain AB [auth C] MOL2 format, chain AC [auth F] MOL2 format, chain BB [auth C] MOL2 format, chain BC [auth F] MOL2 format, chain CB [auth C] MOL2 format, chain CC [auth F] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FC [auth F] MOL2 format, chain GC [auth F] MOL2 format, chain HB [auth C] MOL2 format, chain HC [auth E] MOL2 format, chain IB [auth C] MOL2 format, chain IC [auth E] MOL2 format, chain JB [auth G] MOL2 format, chain JC [auth E] MOL2 format, chain KB [auth G] MOL2 format, chain KC [auth E] MOL2 format, chain LB [auth G] MOL2 format, chain LC [auth E] MOL2 format, chain MB [auth G] MOL2 format, chain NB [auth G] MOL2 format, chain OC [auth E] MOL2 format, chain PC [auth E] MOL2 format, chain QB [auth G] MOL2 format, chain QC [auth D] MOL2 format, chain RB [auth B] MOL2 format, chain RC [auth D] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth B] MOL2 format, chain SC [auth D] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth B] MOL2 format, chain TC [auth D] MOL2 format, chain UA [auth A] MOL2 format, chain UB [auth B] MOL2 format, chain UC [auth D] MOL2 format, chain VA [auth A] MOL2 format, chain VB [auth B] MOL2 format, chain WA [auth A] MOL2 format, chain XC [auth D] MOL2 format, chain YB [auth B] MOL2 format, chain ZA [auth A] MOL2 format, chain ZB [auth F]	AB [auth C] AC [auth F] BB [auth C] BC [auth F] CB [auth C] AB [auth C], AC [auth F], BB [auth C], BC [auth F], CB [auth C], CC [auth F], DB [auth C], EB [auth C], FC [auth F], GC [auth F], HB [auth C], HC [auth E], IB [auth C], IC [auth E], JB [auth G], JC [auth E], KB [auth G], KC [auth E], LB [auth G], LC [auth E], MB [auth G], NB [auth G], OC [auth E], PC [auth E], QB [auth G], QC [auth D], RB [auth B], RC [auth D], SA [auth A], SB [auth B], SC [auth D], TA [auth A], TB [auth B], TC [auth D], UA [auth A], UB [auth B], UC [auth D], VA [auth A], VB [auth B], WA [auth A], XC [auth D], YB [auth B], ZA [auth A], ZB [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain AC [auth F] Focus chain BB [auth C] Focus chain BC [auth F] Focus chain CB [auth C] Focus chain CC [auth F] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FC [auth F] Focus chain GC [auth F] Focus chain HB [auth C] Focus chain HC [auth E] Focus chain IB [auth C] Focus chain IC [auth E] Focus chain JB [auth G] Focus chain JC [auth E] Focus chain KB [auth G] Focus chain KC [auth E] Focus chain LB [auth G] Focus chain LC [auth E] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain OC [auth E] Focus chain PC [auth E] Focus chain QB [auth G] Focus chain QC [auth D] Focus chain RB [auth B] Focus chain RC [auth D] Focus chain SA [auth A] Focus chain SB [auth B] Focus chain SC [auth D] Focus chain TA [auth A] Focus chain TB [auth B] Focus chain TC [auth D] Focus chain UA [auth A] Focus chain UB [auth B] Focus chain UC [auth D] Focus chain VA [auth A] Focus chain VB [auth B] Focus chain WA [auth A] Focus chain XC [auth D] Focus chain YB [auth B] Focus chain ZA [auth A] Focus chain ZB [auth F] Interactions & Density Focus chain AB [auth C] Focus chain AC [auth F] Focus chain BB [auth C] Focus chain BC [auth F] Focus chain CB [auth C] Focus chain CC [auth F] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FC [auth F] Focus chain GC [auth F] Focus chain HB [auth C] Focus chain HC [auth E] Focus chain IB [auth C] Focus chain IC [auth E] Focus chain JB [auth G] Focus chain JC [auth E] Focus chain KB [auth G] Focus chain KC [auth E] Focus chain LB [auth G] Focus chain LC [auth E] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain OC [auth E] Focus chain PC [auth E] Focus chain QB [auth G] Focus chain QC [auth D] Focus chain RB [auth B] Focus chain RC [auth D] Focus chain SA [auth A] Focus chain SB [auth B] Focus chain SC [auth D] Focus chain TA [auth A] Focus chain TB [auth B] Focus chain TC [auth D] Focus chain UA [auth A] Focus chain UB [auth B] Focus chain UC [auth D] Focus chain VA [auth A] Focus chain VB [auth B] Focus chain WA [auth A] Focus chain XC [auth D] Focus chain YB [auth B] Focus chain ZA [auth A] Focus chain ZB [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain DC [auth F] SDF format, chain EC [auth F] SDF format, chain FB [auth C] SDF format, chain GB [auth C] SDF format, chain MC [auth E] SDF format, chain NC [auth E] SDF format, chain OB [auth G] SDF format, chain PB [auth G] SDF format, chain VC [auth D] SDF format, chain WB [auth B] SDF format, chain WC [auth D] SDF format, chain XA [auth A] SDF format, chain XB [auth B] SDF format, chain YA [auth A] MOL2 format, chain DC [auth F] MOL2 format, chain EC [auth F] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain MC [auth E] MOL2 format, chain NC [auth E] MOL2 format, chain OB [auth G] MOL2 format, chain PB [auth G] MOL2 format, chain VC [auth D] MOL2 format, chain WB [auth B] MOL2 format, chain WC [auth D] MOL2 format, chain XA [auth A] MOL2 format, chain XB [auth B] MOL2 format, chain YA [auth A]	DC [auth F] EC [auth F] FB [auth C] GB [auth C] MC [auth E] DC [auth F], EC [auth F], FB [auth C], GB [auth C], MC [auth E], NC [auth E], OB [auth G], PB [auth G], VC [auth D], WB [auth B], WC [auth D], XA [auth A], XB [auth B], YA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DC [auth F] Focus chain EC [auth F] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain MC [auth E] Focus chain NC [auth E] Focus chain OB [auth G] Focus chain PB [auth G] Focus chain VC [auth D] Focus chain WB [auth B] Focus chain WC [auth D] Focus chain XA [auth A] Focus chain XB [auth B] Focus chain YA [auth A] Interactions & Density Focus chain DC [auth F] Focus chain EC [auth F] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain MC [auth E] Focus chain NC [auth E] Focus chain OB [auth G] Focus chain PB [auth G] Focus chain VC [auth D] Focus chain WB [auth B] Focus chain WC [auth D] Focus chain XA [auth A] Focus chain XB [auth B] Focus chain YA [auth A]

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] AA [auth H], BA [auth I], CA [auth J], DA [auth K], EA [auth L], FA [auth M], GA [auth N], H [auth O], HA [auth P], I [auth Q], IA [auth R], J [auth S], JA [auth T], K [auth U], KA [auth V], L [auth W], LA [auth X], M [auth Y], MA [auth Z], N [auth a], NA [auth b], O [auth c], OA [auth d], P [auth e], PA [auth f], Q [auth g], QA [auth h], R [auth i], RA [auth j], S [auth k], T [auth l], U [auth m], V [auth n], W [auth o], X [auth p], Y [auth q], Z [auth r]	lactulose	Oligosaccharide / Water retention		Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain JA [auth j] Focus chain K Focus chain KA [auth k] Focus chain L Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain JA [auth j] Focus chain K Focus chain KA [auth k] Focus chain L Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z

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 Package:

Software Name	Purpose
PHENIX	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

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