1RZO

Agglutinin from Ricinus communis with galactoaza

PDB DOI: https://doi.org/10.2210/pdb1RZO/pdb

Classification: HYDROLASE
Organism(s): Ricinus communis
Mutation(s): No

Deposited: 2003-12-26 Released: 2004-12-28
Deposition Author(s): Gabdoulkhakov, A.G., Savochkina, Y., Konareva, N., Krauspenhaar, R., Stoeva, S., Nikonov, S.V., Voelter, W., Betzel, C., Mikhailov, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free:
0.276 (Depositor)
R-Value Work:
0.225 (Depositor)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Structure-function investigation complex of Agglutinin from Ricinus communis with galactoaza

Gabdoulkhakov, A.G., Savochkina, Y., Konareva, N., Krauspenhaar, R., Stoeva, S., Nikonov, S.V., Voelter, W., Betzel, C., Mikhailov, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 119.82 kDa
Atom Count: 8,759
Modelled Residue Count: 1,043
Deposited Residue Count: 1,048
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agglutinin	A, C	262	Ricinus communis	Mutation(s): 0 EC: 3.2.2.22
UniProt
Find proteins for P06750 (Ricinus communis) Explore P06750 Go to UniProtKB: P06750
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06750
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Agglutinin	B, D	262	Ricinus communis	Mutation(s): 0
UniProt
Find proteins for P06750 (Ricinus communis) Explore P06750 Go to UniProtKB: P06750
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06750
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GAL Query on GAL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D]	E [auth A] I [auth B] J [auth B] K [auth B] L [auth B] E [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], Q [auth C], T [auth D], U [auth D], V [auth D], W [auth D]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D]	F [auth A] G [auth A] H [auth A] N [auth B] O [auth B] F [auth A], G [auth A], H [auth A], N [auth B], O [auth B], P [auth B], R [auth C], S [auth C], X [auth D], Y [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free: 0.276 (Depositor)
R-Value Work: 0.225 (Depositor)
R-Value Observed: 0.225 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.63	α = 90
b = 97.63	β = 90
c = 207.827	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-12-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-12-28
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2016-10-05
Changes: Database references
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.6: 2024-10-30
Changes: Structure summary