9NBG | pdb_00009nbg

H-1 Parvovirus VLP - Glycan [s(Lex)2]

PDB DOI: https://doi.org/10.2210/pdb9NBG/pdb
EM Map EMD-49228: EMDB EMDataResource

Classification: VIRUS LIKE PARTICLE
Organism(s): H-1 parvovirus
Expression System: Baculoviridae sp.
Mutation(s): No

Deposited: 2025-02-13 Released: 2025-07-23
Deposition Author(s): Busuttil, K.B., Bennett, A.B., McKenna, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.57 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Mapping the Sialic Acid Binding Sites of LuIII and H-1 Parvovirus

Busuttil, K.B., Bennett, A.B.

To be published.

Macromolecule Content

Total Structure Weight: 3,785.27 kDa
Atom Count: 267,000
Modeled Residue Count: 33,540
Deposited Residue Count: 33,540
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A AA [auth a] AB [auth 1] B BA [auth b] A, AA [auth a], AB [auth 1], B, BA [auth b], BB [auth 2], C, CA [auth c], CB [auth 3], D, DA [auth d], DB [auth 4], E, EA [auth e], EB [auth 5], F, FA [auth f], FB [auth 6], G, GA [auth g], GB [auth 7], H, HA [auth h], HB [auth 8], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], W, WA [auth w], X, XA [auth x], Y, YA [auth y], Z, ZA [auth z]	559	H-1 parvovirus	Mutation(s): 0
UniProt
Find proteins for P03136 (Hamster parvovirus H1) Explore P03136 Go to UniProtKB: P03136
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03136
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AC [auth aA], AD [auth DB], BC [auth bA], BD [auth EB], CC [auth dA], AC [auth aA], AD [auth DB], BC [auth bA], BD [auth EB], CC [auth dA], CD [auth GB], DC [auth eA], DD [auth HB], EC [auth gA], ED [auth JB], FC [auth hA], FD [auth KB], GC [auth jA], GD [auth MB], HC [auth kA], HD [auth NB], IB [auth 9], IC [auth mA], ID [auth PB], JB [auth AA], JC [auth nA], JD [auth QB], KB [auth CA], KC [auth pA], KD [auth SB], LB [auth DA], LC [auth qA], LD [auth TB], MB [auth FA], MC [auth sA], MD [auth VB], NB [auth GA], NC [auth tA], ND [auth WB], OB [auth IA], OC [auth vA], OD [auth YB], PB [auth JA], PC [auth wA], PD [auth ZB], QB [auth LA], QC [auth yA], RB [auth MA], RC [auth zA], SB [auth OA], SC [auth 1A], TB [auth PA], TC [auth 2A], UB [auth RA], UC [auth 4A], VB [auth SA], VC [auth 5A], WB [auth UA], WC [auth 7A], XB [auth VA], XC [auth 8A], YB [auth XA], YC [auth AB], ZB [auth YA], ZC [auth BB]	3		N/A	Interactions Focus chain AC [auth aA] Focus chain AD [auth DB] Focus chain BC [auth bA] Focus chain BD [auth EB] Focus chain CC [auth dA] Focus chain CD [auth GB] Focus chain DC [auth eA] Focus chain DD [auth HB] Focus chain EC [auth gA] Focus chain ED [auth JB] Focus chain FC [auth hA] Focus chain FD [auth KB] Focus chain GC [auth jA] Focus chain GD [auth MB] Focus chain HC [auth kA] Focus chain HD [auth NB] Focus chain IB [auth 9] Focus chain IC [auth mA] Focus chain ID [auth PB] Focus chain JB [auth AA] Focus chain JC [auth nA] Focus chain JD [auth QB] Focus chain KB [auth CA] Focus chain KC [auth pA] Focus chain KD [auth SB] Focus chain LB [auth DA] Focus chain LC [auth qA] Focus chain LD [auth TB] Focus chain MB [auth FA] Focus chain MC [auth sA] Focus chain MD [auth VB] Focus chain NB [auth GA] Focus chain NC [auth tA] Focus chain ND [auth WB] Focus chain OB [auth IA] Focus chain OC [auth vA] Focus chain OD [auth YB] Focus chain PB [auth JA] Focus chain PC [auth wA] Focus chain PD [auth ZB] Focus chain QB [auth LA] Focus chain QC [auth yA] Focus chain RB [auth MA] Focus chain RC [auth zA] Focus chain SB [auth OA] Focus chain SC [auth 1A] Focus chain TB [auth PA] Focus chain TC [auth 2A] Focus chain UB [auth RA] Focus chain UC [auth 4A] Focus chain VB [auth SA] Focus chain VC [auth 5A] Focus chain WB [auth UA] Focus chain WC [auth 7A] Focus chain XB [auth VA] Focus chain XC [auth 8A] Focus chain YB [auth XA] Focus chain YC [auth AB] Focus chain ZB [auth YA] Focus chain ZC [auth BB] Interactions & Density Focus chain AC [auth aA] Focus chain AD [auth DB] Focus chain BC [auth bA] Focus chain BD [auth EB] Focus chain CC [auth dA] Focus chain CD [auth GB] Focus chain DC [auth eA] Focus chain DD [auth HB] Focus chain EC [auth gA] Focus chain ED [auth JB] Focus chain FC [auth hA] Focus chain FD [auth KB] Focus chain GC [auth jA] Focus chain GD [auth MB] Focus chain HC [auth kA] Focus chain HD [auth NB] Focus chain IB [auth 9] Focus chain IC [auth mA] Focus chain ID [auth PB] Focus chain JB [auth AA] Focus chain JC [auth nA] Focus chain JD [auth QB] Focus chain KB [auth CA] Focus chain KC [auth pA] Focus chain KD [auth SB] Focus chain LB [auth DA] Focus chain LC [auth qA] Focus chain LD [auth TB] Focus chain MB [auth FA] Focus chain MC [auth sA] Focus chain MD [auth VB] Focus chain NB [auth GA] Focus chain NC [auth tA] Focus chain ND [auth WB] Focus chain OB [auth IA] Focus chain OC [auth vA] Focus chain OD [auth YB] Focus chain PB [auth JA] Focus chain PC [auth wA] Focus chain PD [auth ZB] Focus chain QB [auth LA] Focus chain QC [auth yA] Focus chain RB [auth MA] Focus chain RC [auth zA] Focus chain SB [auth OA] Focus chain SC [auth 1A] Focus chain TB [auth PA] Focus chain TC [auth 2A] Focus chain UB [auth RA] Focus chain UC [auth 4A] Focus chain VB [auth SA] Focus chain VC [auth 5A] Focus chain WB [auth UA] Focus chain WC [auth 7A] Focus chain XB [auth VA] Focus chain XC [auth 8A] Focus chain YB [auth XA] Focus chain YC [auth AB] Focus chain ZB [auth YA] Focus chain ZC [auth BB]
Glycosylation Resources
GlyTouCan: G57474XD GlyCosmos: G57474XD GlyGen: G57474XD

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900067 Query on PRD_900067	AC [auth 1A] AD [auth 2A] BC [auth 4A] BD [auth 5A] CC [auth 7A] AC [auth 1A], AD [auth 2A], BC [auth 4A], BD [auth 5A], CC [auth 7A], CD [auth 8A], DC [auth 9], DD [auth AA], EC [auth AB], ED [auth BB], FC [auth CA], FD [auth DA], GC [auth DB], GD [auth EB], HC [auth FA], HD [auth GA], IB [auth GB], IC [auth HB], ID [auth IA], JB [auth JA], JC [auth JB], JD [auth KB], KB [auth LA], KC [auth MA], KD [auth MB], LB [auth NB], LC [auth OA], LD [auth PA], MB [auth PB], MC [auth QB], MD [auth RA], NB [auth SA], NC [auth SB], ND [auth TB], OB [auth UA], OC [auth VA], OD [auth VB], PB [auth WB], PC [auth XA], PD [auth YA], QB [auth YB], QC [auth ZB], RB [auth aA], RC [auth bA], SB [auth dA], SC [auth eA], TB [auth gA], TC [auth hA], UB [auth jA], UC [auth kA], VB [auth mA], VC [auth nA], WB [auth pA], WC [auth qA], XB [auth sA], XC [auth tA], YB [auth vA], YC [auth wA], ZB [auth yA], ZC [auth zA]	3'-sialyl-N-acetyllactosamine	Oligosaccharide / Substrate analog		Interactions Focus chain AC [auth aA] Focus chain AD [auth DB] Focus chain BC [auth bA] Focus chain BD [auth EB] Focus chain CC [auth dA] Focus chain CD [auth GB] Focus chain DC [auth eA] Focus chain DD [auth HB] Focus chain EC [auth gA] Focus chain ED [auth JB] Focus chain FC [auth hA] Focus chain FD [auth KB] Focus chain GC [auth jA] Focus chain GD [auth MB] Focus chain HC [auth kA] Focus chain HD [auth NB] Focus chain IB [auth 9] Focus chain IC [auth mA] Focus chain ID [auth PB] Focus chain JB [auth AA] Focus chain JC [auth nA] Focus chain JD [auth QB] Focus chain KB [auth CA] Focus chain KC [auth pA] Focus chain KD [auth SB] Focus chain LB [auth DA] Focus chain LC [auth qA] Focus chain LD [auth TB] Focus chain MB [auth FA] Focus chain MC [auth sA] Focus chain MD [auth VB] Focus chain NB [auth GA] Focus chain NC [auth tA] Focus chain ND [auth WB] Focus chain OB [auth IA] Focus chain OC [auth vA] Focus chain OD [auth YB] Focus chain PB [auth JA] Focus chain PC [auth wA] Focus chain PD [auth ZB] Focus chain QB [auth LA] Focus chain QC [auth yA] Focus chain RB [auth MA] Focus chain RC [auth zA] Focus chain SB [auth OA] Focus chain SC [auth 1A] Focus chain TB [auth PA] Focus chain TC [auth 2A] Focus chain UB [auth RA] Focus chain UC [auth 4A] Focus chain VB [auth SA] Focus chain VC [auth 5A] Focus chain WB [auth UA] Focus chain WC [auth 7A] Focus chain XB [auth VA] Focus chain XC [auth 8A] Focus chain YB [auth XA] Focus chain YC [auth AB] Focus chain ZB [auth YA] Focus chain ZC [auth BB] Interactions & Density Focus chain AC [auth aA] Focus chain AD [auth DB] Focus chain BC [auth bA] Focus chain BD [auth EB] Focus chain CC [auth dA] Focus chain CD [auth GB] Focus chain DC [auth eA] Focus chain DD [auth HB] Focus chain EC [auth gA] Focus chain ED [auth JB] Focus chain FC [auth hA] Focus chain FD [auth KB] Focus chain GC [auth jA] Focus chain GD [auth MB] Focus chain HC [auth kA] Focus chain HD [auth NB] Focus chain IB [auth 9] Focus chain IC [auth mA] Focus chain ID [auth PB] Focus chain JB [auth AA] Focus chain JC [auth nA] Focus chain JD [auth QB] Focus chain KB [auth CA] Focus chain KC [auth pA] Focus chain KD [auth SB] Focus chain LB [auth DA] Focus chain LC [auth qA] Focus chain LD [auth TB] Focus chain MB [auth FA] Focus chain MC [auth sA] Focus chain MD [auth VB] Focus chain NB [auth GA] Focus chain NC [auth tA] Focus chain ND [auth WB] Focus chain OB [auth IA] Focus chain OC [auth vA] Focus chain OD [auth YB] Focus chain PB [auth JA] Focus chain PC [auth wA] Focus chain PD [auth ZB] Focus chain QB [auth LA] Focus chain QC [auth yA] Focus chain RB [auth MA] Focus chain RC [auth zA] Focus chain SB [auth OA] Focus chain SC [auth 1A] Focus chain TB [auth PA] Focus chain TC [auth 2A] Focus chain UB [auth RA] Focus chain UC [auth 4A] Focus chain VB [auth SA] Focus chain VC [auth 5A] Focus chain WB [auth UA] Focus chain WC [auth 7A] Focus chain XB [auth VA] Focus chain XC [auth 8A] Focus chain YB [auth XA] Focus chain YC [auth AB] Focus chain ZB [auth YA] Focus chain ZC [auth BB]