2GMM

Metal-free (apo) P. angolensis seed lectin in complex with Man-alpha(1-2)Man

PDB DOI: https://doi.org/10.2210/pdb2GMM/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Pterocarpus angolensis
Mutation(s): No

Deposited: 2006-04-07 Released: 2006-07-25
Deposition Author(s): Garcia-Pino, A., Buts, L., Wyns, L., Loris, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.227
R-Value Work: 0.185
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 55.99 kDa
Atom Count: 3,817
Modelled Residue Count: 459
Deposited Residue Count: 504
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	252	Pterocarpus angolensis	Mutation(s): 0
UniProt
Find proteins for Q8GSD2 (Pterocarpus angolensis) Explore Q8GSD2 Go to UniProtKB: Q8GSD2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8GSD2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	C, D	2		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G53402KW GlyCosmos: G53402KW GlyGen: G53402KW

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B]	E [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A, B	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900111 Query on PRD_900111	C, D	2alpha-alpha-mannobiose	Oligosaccharide / Metabolism		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.227
R-Value Work: 0.185
R-Value Observed: 0.188
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.706	α = 90
b = 62.587	β = 90
c = 129.959	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-07-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-07-25
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-02-14
Changes: Experimental preparation
Version 2.0: 2019-12-25
Changes: Data collection, Database references, Derived calculations, Polymer sequence
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary

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Help and Resources

2GMM

Metal-free (apo) P. angolensis seed lectin in complex with Man-alpha(1-2)Man

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Entity ID: 2

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)