6VL5

BG505 SOSIP reconstructed from a designed tetrahedral nanoparticle, BG505 SOSIP-T33_dn2

PDB DOI: https://doi.org/10.2210/pdb6VL5/pdb
EM Map EMD-21230: EMDB EMDataResource

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-01-22 Released: 2020-08-12
Deposition Author(s): Ward, A.B., Antanasijevic, A.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 249.49 kDa
Atom Count: 15,039
Modelled Residue Count: 1,719
Deposited Residue Count: 2,016
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 SOSIP.v5.2(7S) - gp120	A [auth C], C [auth A], E	506	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 SOSIP.v5.2(7S) - gp41	B [auth D], D [auth B], F	166	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
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)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], G, Q	5		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain G Focus chain Q Interactions & Density Focus chain AA [auth a] Focus chain G Focus chain Q
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, L, M, N, O, P, R, S, T, U, V, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain JA [auth j] Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain JA [auth j] Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z
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 AB [auth A] SDF format, chain BB [auth A] SDF format, chain CB [auth A] SDF format, chain DB [auth A] SDF format, chain EB [auth A] SDF format, chain FB [auth B] SDF format, chain GB [auth B] SDF format, chain HB [auth B] SDF format, chain IB [auth E] SDF format, chain JB [auth E] SDF format, chain KA [auth C] SDF format, chain KB [auth E] SDF format, chain LA [auth C] SDF format, chain LB [auth E] SDF format, chain MA [auth C] SDF format, chain MB [auth E] SDF format, chain NA [auth C] SDF format, chain NB [auth E] SDF format, chain OA [auth C] SDF format, chain OB [auth E] SDF format, chain PA [auth C] SDF format, chain PB [auth E] SDF format, chain QA [auth C] SDF format, chain QB [auth E] SDF format, chain RA [auth C] SDF format, chain RB [auth F] SDF format, chain SA [auth C] SDF format, chain SB [auth F] SDF format, chain TA [auth D] SDF format, chain TB [auth F] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain WA [auth A] SDF format, chain XA [auth A] SDF format, chain YA [auth A] SDF format, chain ZA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain CB [auth A] MOL2 format, chain DB [auth A] MOL2 format, chain EB [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain GB [auth B] MOL2 format, chain HB [auth B] MOL2 format, chain IB [auth E] MOL2 format, chain JB [auth E] MOL2 format, chain KA [auth C] MOL2 format, chain KB [auth E] MOL2 format, chain LA [auth C] MOL2 format, chain LB [auth E] MOL2 format, chain MA [auth C] MOL2 format, chain MB [auth E] MOL2 format, chain NA [auth C] MOL2 format, chain NB [auth E] MOL2 format, chain OA [auth C] MOL2 format, chain OB [auth E] MOL2 format, chain PA [auth C] MOL2 format, chain PB [auth E] MOL2 format, chain QA [auth C] MOL2 format, chain QB [auth E] MOL2 format, chain RA [auth C] MOL2 format, chain RB [auth F] MOL2 format, chain SA [auth C] MOL2 format, chain SB [auth F] MOL2 format, chain TA [auth D] MOL2 format, chain TB [auth F] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain ZA [auth A]	AB [auth A] BB [auth A] CB [auth A] DB [auth A] EB [auth A] AB [auth A], BB [auth A], CB [auth A], DB [auth A], EB [auth A], FB [auth B], GB [auth B], HB [auth B], IB [auth E], JB [auth E], KA [auth C], KB [auth E], LA [auth C], LB [auth E], MA [auth C], MB [auth E], NA [auth C], NB [auth E], OA [auth C], OB [auth E], PA [auth C], PB [auth E], QA [auth C], QB [auth E], RA [auth C], RB [auth F], SA [auth C], SB [auth F], TA [auth D], TB [auth F], UA [auth D], VA [auth D], WA [auth A], XA [auth A], YA [auth A], ZA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth A] Focus chain BB [auth A] Focus chain CB [auth A] Focus chain DB [auth A] Focus chain EB [auth A] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain KA [auth C] Focus chain KB [auth E] Focus chain LA [auth C] Focus chain LB [auth E] Focus chain MA [auth C] Focus chain MB [auth E] Focus chain NA [auth C] Focus chain NB [auth E] Focus chain OA [auth C] Focus chain OB [auth E] Focus chain PA [auth C] Focus chain PB [auth E] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain RA [auth C] Focus chain RB [auth F] Focus chain SA [auth C] Focus chain SB [auth F] Focus chain TA [auth D] Focus chain TB [auth F] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain AB [auth A] Focus chain BB [auth A] Focus chain CB [auth A] Focus chain DB [auth A] Focus chain EB [auth A] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain KA [auth C] Focus chain KB [auth E] Focus chain LA [auth C] Focus chain LB [auth E] Focus chain MA [auth C] Focus chain MB [auth E] Focus chain NA [auth C] Focus chain NB [auth E] Focus chain OA [auth C] Focus chain OB [auth E] Focus chain PA [auth C] Focus chain PB [auth E] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain RA [auth C] Focus chain RB [auth F] Focus chain SA [auth C] Focus chain SB [auth F] Focus chain TA [auth D] Focus chain TB [auth F] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A]