6PDL

Crystal Structure of Hendra Virus Attachment G Glycoprotein in Complex with Receptor Ephrin-B2

PDB DOI: https://doi.org/10.2210/pdb6PDL/pdb

Classification: VIRAL PROTEIN/SIGNALING PROTEIN
Organism(s): Henipavirus hendraense, Homo sapiens
Expression System: Insect cell expression vector pTIE1
Mutation(s): No

Deposited: 2019-06-19 Released: 2019-11-27
Deposition Author(s): Xu, K., Nikolov, D.B.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.227
R-Value Work: 0.172
R-Value Observed: 0.175

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: 273.22 kDa
Atom Count: 18,707
Modelled Residue Count: 2,222
Deposited Residue Count: 2,328
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Attachment glycoprotein	A, C, E, G	441	Henipavirus hendraense	Mutation(s): 0
UniProt
Find proteins for O89343 (Hendra virus (isolate Horse/Autralia/Hendra/1994)) Explore O89343 Go to UniProtKB: O89343
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O89343
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin-B2	B, D, F, H	141	Homo sapiens	Mutation(s): 0 Gene Names: EFNB2, EPLG5, HTKL, LERK5
UniProt & NIH Common Fund Data Resources
Find proteins for P52799 (Homo sapiens) Explore P52799 Go to UniProtKB: P52799
PHAROS: P52799 GTEx: ENSG00000125266
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P52799
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)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, J, L, M, P I, J, L, M, P, S	2		N-Glycosylation	Interactions Focus chain I Focus chain J Focus chain L Focus chain M Focus chain P Focus chain S Interactions & Density Focus chain I Focus chain J Focus chain L Focus chain M Focus chain P Focus chain S
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	K, T	7		N-Glycosylation	Interactions Focus chain K Focus chain T Interactions & Density Focus chain K Focus chain T
Glycosylation Resources
GlyTouCan: G11460AB GlyCosmos: G11460AB GlyGen: G11460AB

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	N	7		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
Glycosylation Resources
GlyTouCan: G47385JB GlyCosmos: G47385JB GlyGen: G47385JB

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O, R	3		N-Glycosylation	Interactions Focus chain O Focus chain R Interactions & Density Focus chain O Focus chain R
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
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)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	Q	5		N-Glycosylation	Interactions Focus chain Q Interactions & Density Focus chain Q
Glycosylation Resources
GlyTouCan: G92953ND GlyCosmos: G92953ND

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain Z [auth D] SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain CA [auth F] SDF format, chain DA [auth G] SDF format, chain EA [auth G] SDF format, chain FA [auth H] SDF format, chain GA [auth H] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C]	AA [auth E] BA [auth E] CA [auth F] DA [auth G] EA [auth G] AA [auth E], BA [auth E], CA [auth F], DA [auth G], EA [auth G], FA [auth H], GA [auth H], U [auth A], V [auth A], W [auth B], X [auth C], Y [auth C], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.227
R-Value Work: 0.172
R-Value Observed: 0.175
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.764	α = 112.86
b = 94.642	β = 97.44
c = 102.522	γ = 97.56

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-11-27

Deposition Author(s):

Xu, K.

Nikolov, D.B.

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	NS38486
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	AI057168
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	AI054715

Revision History (Full details and data files)

Version 1.0: 2019-11-27
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary