1BQP | pdb_00001bqp

THE STRUCTURE OF THE PEA LECTIN-D-MANNOPYRANOSE COMPLEX

PDB DOI: https://doi.org/10.2210/pdb1BQP/pdb

Classification: PLANT PROTEIN
Organism(s): Lathyrus oleraceus
Mutation(s): No

Deposited: 1998-08-17 Released: 1998-08-26
Deposition Author(s): Ruzeinikov, S.N., Mikhailova, I.Y., Tsygannik, I.N., Pangborn, W., Duax, W., Pletnev, V.Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.188 (Depositor)
R-Value Work:
0.161 (Depositor)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

The Structure of the Pea Lectin-D-Mannopyranose Complex at a 2.1 A Resolution

Ruzheinikov, S.N., Mikhailova, I.Y., Tsygannik, I.N., Pangborn, W., Duax, W., Pletnev, V.Z.

(1998) Russ J Bioorg Chem 24: 277-279

Macromolecule Content

Total Structure Weight: 51.27 kDa
Atom Count: 3,878
Modeled Residue Count: 456
Deposited Residue Count: 456
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (LECTIN)	A, C	181	Lathyrus oleraceus	Mutation(s): 0
UniProt
Find proteins for P02867 (Pisum sativum) Explore P02867 Go to UniProtKB: P02867
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02867
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (LECTIN)	B, D	47	Lathyrus oleraceus	Mutation(s): 0
UniProt
Find proteins for P02867 (Pisum sativum) Explore P02867 Go to UniProtKB: P02867
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02867
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BMA Query on BMA Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C]	H [auth B], K [auth C]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain H [auth B] Focus chain K [auth C]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B]	G [auth B], I [auth C]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain G [auth B] Focus chain I [auth C]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain L [auth C]	F [auth A], L [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth C]	E [auth A], J [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.188 (Depositor)
R-Value Work: 0.161 (Depositor)
R-Value Observed: 0.161 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.926	α = 90
b = 104.083	β = 90
c = 64.837	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 1998-08-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1998-08-26
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2016-02-17
Changes: Non-polymer description
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2023-08-09
Changes: Data collection, Database references, Refinement description, Structure summary