4M3C | pdb_00004m3c

Structure of a binary complex between homologous tetrameric legume lectins from Butea monosperma and Spatholobus parviflorus seeds

PDB DOI: https://doi.org/10.2210/pdb4M3C/pdb

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

Deposited: 2013-08-06 Released: 2013-09-18
Deposition Author(s): Surya, S., Abhilash, J., Geethanandan, K., Sadasivan, C., Haridas, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.289 (Depositor), 0.288 (DCC)
R-Value Work:
0.211 (Depositor), 0.211 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 3.0 of the entry. See complete history.

Literature

Structure of a binary complex between homologous tetrameric legume lectins from Butea monosperma and Spatholobus parviflorus seeds

Surya, S., Abhilash, J., Geethanandan, K., Sadasivan, C., Haridas, M.

To be published.

Macromolecule Content

Total Structure Weight: 210.26 kDa
Atom Count: 15,035
Modeled Residue Count: 1,952
Deposited Residue Count: 1,968
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin Alpha chain	A, C	255	Butea monosperma	Mutation(s): 0
UniProt
Find proteins for H2L2M6 (Butea monosperma) Explore H2L2M6 Go to UniProtKB: H2L2M6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H2L2M6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin Beta Chain	B, D	239	Butea monosperma	Mutation(s): 0
UniProt
Find proteins for H2L2M7 (Butea monosperma) Explore H2L2M7 Go to UniProtKB: H2L2M7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H2L2M7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Seed lectin alpha chain	E, G	251	Spatholobus parviflorus	Mutation(s): 0
UniProt
Find proteins for P86352 (Spatholobus parviflorus) Explore P86352 Go to UniProtKB: P86352
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P86352
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Seed lectin beta chain	F, H	239	Spatholobus parviflorus	Mutation(s): 0
UniProt
Find proteins for P86353 (Spatholobus parviflorus) Explore P86353 Go to UniProtKB: P86353
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P86353
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ABU Query on ABU Download:Ideal Coordinates CCD File SDF format, chain GA [auth H] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain Y [auth E] MOL2 format, chain GA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain GA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Y [auth E]	GA [auth H] K [auth A] N [auth B] Q [auth C] U [auth D] GA [auth H], K [auth A], N [auth B], Q [auth C], U [auth D], Y [auth E]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain GA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain GA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain BA [auth F] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain BA [auth F] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D] mmCIF format, chain BA [auth F]	BA [auth F], R [auth C], V [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain BA [auth F] Focus chain R [auth C] Focus chain V [auth D]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain DA [auth G] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain X [auth E] SDF format, chain FA [auth H] MOL2 format, chain AA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain X [auth E] MOL2 format, chain FA [auth H] mmCIF format, chain AA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain X [auth E] mmCIF format, chain FA [auth H]	AA [auth F] DA [auth G] FA [auth H] J [auth A] M [auth B] AA [auth F], DA [auth G], FA [auth H], J [auth A], M [auth B], P [auth C], T [auth D], X [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain EA [auth H] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain Z [auth F] SDF format, chain W [auth E] SDF format, chain CA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain Z [auth F] MOL2 format, chain W [auth E] MOL2 format, chain CA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain Z [auth F] mmCIF format, chain W [auth E] mmCIF format, chain CA [auth G]	CA [auth G] EA [auth H] I [auth A] L [auth B] O [auth C] CA [auth G], EA [auth H], I [auth A], L [auth B], O [auth C], S [auth D], W [auth E], Z [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.289 (Depositor), 0.288 (DCC)
R-Value Work: 0.211 (Depositor), 0.211 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.11	α = 96
b = 78.63	β = 89.99
c = 96.19	γ = 100.37

Software Package:

Software Name	Purpose
MAR345dtb	data collection
Auto	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
Auto	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-09-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-18
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations
Version 3.0: 2024-01-31
Changes: Atomic model