3USU | pdb_00003usu

Crystal structure of Butea monosperma seed lectin

PDB DOI: https://doi.org/10.2210/pdb3USU/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Butea monosperma
Mutation(s): No

Deposited: 2011-11-24 Released: 2012-01-04
Deposition Author(s): Abhilash, J., Geethanandan, K., Bharath, S.R., Sadasivan, C., Haridas, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free:
0.287 (Depositor), 0.290 (DCC)
R-Value Work:
0.205 (Depositor), 0.210 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Literature

Crystal structure of Butea monosperma seed lectin

Abhilash, J., Geethanandan, K., Bharath, S.R., Sadasivan, C., Haridas, M.

To be published.

Macromolecule Content

Total Structure Weight: 218.76 kDa
Atom Count: 15,748
Modeled Residue Count: 1,968
Deposited Residue Count: 1,992
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin Alpha chain	A, C, E, G	256	Butea monosperma	Mutation(s): 0
UniProt
Find proteins for H2L2M6 (Butea monosperma) Explore H2L2M6 Go to UniProtKB: H2L2M6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	H2L2M6
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain C Focus chain E Focus chain G
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin Beta Chain	B, D, F, H	242	Butea monosperma	Mutation(s): 0
UniProt
Find proteins for H2L2M6 (Butea monosperma) Explore H2L2M6 Go to UniProtKB: H2L2M6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	H2L2M6
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D Focus chain H
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	I, K, L	4		N-Glycosylation	Interactions Focus chain I Focus chain K Focus chain L Interactions & Density Focus chain I Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G18638YB GlyCosmos: G18638YB GlyGen: G18638YB

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	J	5		N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G17689EW GlyCosmos: G17689EW GlyGen: G17689EW

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M	2		N-Glycosylation	Interactions Focus chain M Interactions & Density Focus chain M
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	N	2		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
Glycosylation Resources
GlyTouCan: G80587NA GlyCosmos: G80587NA GlyGen: G80587NA

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain FA [auth D] MOL2 format, chain FA [auth D] mmCIF format, chain FA [auth D]	FA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain FA [auth D] Interactions & Density Focus chain FA [auth D]
XYP Query on XYP Download Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	beta-D-xylopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-KKQCNMDGSA-N		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]
ABU Query on ABU Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain EA [auth D] SDF format, chain JA [auth E] SDF format, chain LA [auth E] SDF format, chain OA [auth F] SDF format, chain Q [auth A] SDF format, chain SA [auth G] SDF format, chain V [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain OA [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain SA [auth G] MOL2 format, chain V [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain LA [auth E] mmCIF format, chain OA [auth F] mmCIF format, chain Q [auth A] mmCIF format, chain SA [auth G] mmCIF format, chain V [auth B]	AA [auth C] EA [auth D] JA [auth E] LA [auth E] OA [auth F] AA [auth C], EA [auth D], JA [auth E], LA [auth E], OA [auth F], Q [auth A], SA [auth G], V [auth B]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain EA [auth D] Focus chain JA [auth E] Focus chain LA [auth E] Focus chain OA [auth F] Focus chain Q [auth A] Focus chain SA [auth G] Focus chain V [auth B] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth D] Focus chain JA [auth E] Focus chain LA [auth E] Focus chain OA [auth F] Focus chain Q [auth A] Focus chain SA [auth G] Focus chain V [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain IA [auth E] SDF format, chain KA [auth E] SDF format, chain R [auth A] SDF format, chain RA [auth G] SDF format, chain S [auth B] SDF format, chain VA [auth H] SDF format, chain Z [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain VA [auth H] MOL2 format, chain Z [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain VA [auth H] mmCIF format, chain Z [auth C]	DA [auth D] IA [auth E] KA [auth E] R [auth A] RA [auth G] DA [auth D], IA [auth E], KA [auth E], R [auth A], RA [auth G], S [auth B], VA [auth H], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain IA [auth E] Focus chain KA [auth E] Focus chain R [auth A] Focus chain RA [auth G] Focus chain S [auth B] Focus chain VA [auth H] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain IA [auth E] Focus chain KA [auth E] Focus chain R [auth A] Focus chain RA [auth G] Focus chain S [auth B] Focus chain VA [auth H] Focus chain Z [auth C]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain HA [auth E] SDF format, chain NA [auth F] SDF format, chain P [auth A] SDF format, chain QA [auth G] SDF format, chain U [auth B] SDF format, chain UA [auth H] SDF format, chain Y [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain NA [auth F] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth G] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth H] MOL2 format, chain Y [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain NA [auth F] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth G] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth H] mmCIF format, chain Y [auth C]	CA [auth D] HA [auth E] NA [auth F] P [auth A] QA [auth G] CA [auth D], HA [auth E], NA [auth F], P [auth A], QA [auth G], U [auth B], UA [auth H], Y [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain HA [auth E] Focus chain NA [auth F] Focus chain P [auth A] Focus chain QA [auth G] Focus chain U [auth B] Focus chain UA [auth H] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth D] Focus chain HA [auth E] Focus chain NA [auth F] Focus chain P [auth A] Focus chain QA [auth G] Focus chain U [auth B] Focus chain UA [auth H] Focus chain Y [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain GA [auth E] SDF format, chain MA [auth F] SDF format, chain O [auth A] SDF format, chain PA [auth G] SDF format, chain T [auth B] SDF format, chain TA [auth H] SDF format, chain X [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain MA [auth F] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth G] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth H] MOL2 format, chain X [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain MA [auth F] mmCIF format, chain O [auth A] mmCIF format, chain PA [auth G] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth H] mmCIF format, chain X [auth C]	BA [auth D] GA [auth E] MA [auth F] O [auth A] PA [auth G] BA [auth D], GA [auth E], MA [auth F], O [auth A], PA [auth G], T [auth B], TA [auth H], X [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain GA [auth E] Focus chain MA [auth F] Focus chain O [auth A] Focus chain PA [auth G] Focus chain T [auth B] Focus chain TA [auth H] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain GA [auth E] Focus chain MA [auth F] Focus chain O [auth A] Focus chain PA [auth G] Focus chain T [auth B] Focus chain TA [auth H] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.287 (Depositor), 0.290 (DCC)
R-Value Work: 0.205 (Depositor), 0.210 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.45	α = 74.3
b = 78.91	β = 76.65
c = 101.85	γ = 86.88

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-01-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-01-04
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
Version 3.0: 2023-11-15
Changes: Atomic model, Data collection
Version 3.1: 2024-11-20
Changes: Structure summary