6EG1

Crystal structure of Dpr2 Ig1-Ig2 in complex with DIP-Theta Ig1-Ig3

PDB DOI: https://doi.org/10.2210/pdb6EG1/pdb

Classification: CELL ADHESION
Organism(s): Drosophila melanogaster
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2018-08-17 Released: 2018-11-28
Deposition Author(s): Cosmanescu, F., Patel, S., Shapiro, L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.231
R-Value Work: 0.178
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 127.65 kDa
Atom Count: 8,665
Modelled Residue Count: 1,029
Deposited Residue Count: 1,066
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Defective proboscis extension response 2, isoform F	A, C	231	Drosophila melanogaster	Mutation(s): 0 Gene Names: dpr2, BP1042, CG14067, CG14068, CT33638, Dmel\CG33507, Dpr-2, Dpr2, CG33507, Dmel_CG33507
UniProt
Find proteins for Q59DZ4 (Drosophila melanogaster) Explore Q59DZ4 Go to UniProtKB: Q59DZ4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q59DZ4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dpr-interacting protein theta	B, D	302	Drosophila melanogaster	Mutation(s): 0 Gene Names: DIP-theta, 31646, CG14008, CG14009, CG31646-RA, CT33566, Dmel\CG31646, CG31646, Dmel_CG31646
UniProt
Find proteins for Q9VMN6 (Drosophila melanogaster) Explore Q9VMN6 Go to UniProtKB: Q9VMN6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9VMN6
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E, I, J, K, N	3		N-Glycosylation	Interactions Focus chain E Focus chain I Focus chain J Focus chain K Focus chain N Interactions & Density Focus chain E Focus chain I Focus chain J Focus chain K Focus chain N
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

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-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F, L	5		N-Glycosylation	Interactions Focus chain F Focus chain L Interactions & Density Focus chain F Focus chain L
Glycosylation Resources
GlyTouCan: G42466VF GlyCosmos: G42466VF GlyGen: G42466VF

Entity ID: 5
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-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G, M	4		N-Glycosylation	Interactions Focus chain G Focus chain M Interactions & Density Focus chain G Focus chain M
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	2		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O	2		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain U [auth D] MOL2 format, chain U [auth D]	U [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain U [auth D] Interactions & Density Focus chain U [auth D]
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C]	P [auth C], Q [auth C]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain P [auth C] Focus chain Q [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D]	R [auth C], V [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain R [auth C] Focus chain V [auth D]
BU3 Query on BU3 Download Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C]	S [auth C], T [auth C]	(R,R)-2,3-BUTANEDIOL C₄ H₁₀ O₂ OWBTYPJTUOEWEK-QWWZWVQMSA-N		Interactions Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain S [auth C] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.231
R-Value Work: 0.178
R-Value Observed: 0.180
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.771	α = 90
b = 120.908	β = 90
c = 144.908	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-11-28

Deposition Author(s):

Cosmanescu, F.

Patel, S.

Shapiro, L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2018-11-28
Type: Initial release
Version 1.1: 2018-12-19
Changes: Data collection, Database references
Version 1.2: 2019-01-02
Changes: Data collection, Database references
Version 1.3: 2019-08-21
Changes: Data collection, Structure summary
Version 1.4: 2020-01-01
Changes: Author supporting evidence, Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary