6V48

The crystal structure of hemagglutinin from A/mallard/Gurjev/263/1982 (H14N5)

PDB DOI: https://doi.org/10.2210/pdb6V48/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/mallard/Astrakhan/263/1982(H14N5))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2019-11-27 Released: 2020-06-17
Deposition Author(s): Yang, H., Stevens, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.260
R-Value Work: 0.224
R-Value Observed: 0.226

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

Macromolecule Content

Total Structure Weight: 354.57 kDa
Atom Count: 23,322
Modelled Residue Count: 2,922
Deposited Residue Count: 3,138
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, C, E, G, I A, C, E, G, I, K	335	Influenza A virus (A/mallard/Astrakhan/263/1982(H14N5))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for P26136 (Influenza A virus (strain A/Mallard/Astrakhan/263/1982 H14N5)) Explore P26136 Go to UniProtKB: P26136
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P26136
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B, D, F, H, J B, D, F, H, J, L	188	Influenza A virus (A/mallard/Astrakhan/263/1982(H14N5))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for P26136 (Influenza A virus (strain A/Mallard/Astrakhan/263/1982 H14N5)) Explore P26136 Go to UniProtKB: P26136
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P26136
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	M, N, O, P, Q M, N, O, P, Q, R, S, T, U, V, W, X	2		N-Glycosylation	Interactions Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 AA [auth E] SDF format, chain BA [auth G] SDF format, chain CA [auth I] SDF format, chain DA [auth K] SDF format, chain Y [auth A] SDF format, chain Z [auth C] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth K] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth C]	AA [auth E] BA [auth G] CA [auth I] DA [auth K] Y [auth A] AA [auth E], BA [auth G], CA [auth I], DA [auth K], Y [auth A], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth G] Focus chain CA [auth I] Focus chain DA [auth K] Focus chain Y [auth A] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth G] Focus chain CA [auth I] Focus chain DA [auth K] Focus chain Y [auth A] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.260
R-Value Work: 0.224
R-Value Observed: 0.226
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.665	α = 90
b = 100.974	β = 103.93
c = 236.075	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-06-17

Deposition Author(s):

Yang, H.

Stevens, J.

Revision History (Full details and data files)

Version 1.0: 2020-06-17
Type: Initial release
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, Refinement description, Structure summary

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6V48

The crystal structure of hemagglutinin from A/mallard/Gurjev/263/1982 (H14N5)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2