1SFY

Crystal structure of recombinant Erythrina corallodandron Lectin

PDB DOI: https://doi.org/10.2210/pdb1SFY/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Erythrina corallodendron
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-02-21 Released: 2004-08-10
Deposition Author(s): Kulkarni, K.A., Srivastava, A., Mitra, N., Surolia, A., Vijayan, M., Suguna, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.208
R-Value Work: 0.180
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 160.23 kDa
Atom Count: 12,073
Modelled Residue Count: 1,434
Deposited Residue Count: 1,434
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	A, B, C, D, E A, B, C, D, E, F	239	Erythrina corallodendron	Mutation(s): 0
UniProt
Find proteins for P16404 (Erythrina corallodendron) Explore P16404 Go to UniProtKB: P16404
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16404
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	G, H, I, J, K G, H, I, J, K, L	2		N/A	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G84224TW GlyCosmos: G84224TW GlyGen: G84224TW

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F]	M [auth A] O [auth B] Q [auth C] S [auth D] U [auth E] M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Interactions & Density Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain V [auth E] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain X [auth F] MOL2 format, chain V [auth E] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain X [auth F]	N [auth A] P [auth B] R [auth C] T [auth D] V [auth E] N [auth A], P [auth B], R [auth C], T [auth D], V [auth E], X [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Interactions & Density Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004 Query on PRD_900004	G, H, I, J, K G, H, I, J, K, L	beta-lactose	Oligosaccharide / Nutrient		Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.208
R-Value Work: 0.180
R-Value Observed: 0.180
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.24	α = 90
b = 144.89	β = 93.29
c = 127.66	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-08-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-08-10
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary

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Deposit Data

Help and Resources

1SFY

Crystal structure of recombinant Erythrina corallodandron Lectin

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 2

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)