9GST | pdb_00009gst

LN02-ML85 Fab in complex with crosslinked DS-SOSIP HIV-1 Env trimer

PDB DOI: https://doi.org/10.2210/pdb9GST/pdb
EM Map EMD-51554: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-09-16 Released: 2025-09-24
Deposition Author(s): Pedenko, B., Effantin, G., Weissenhorn, W.
Funding Organization(s): Grenoble Alliance for Integrated Structural Cell Biology (GRAL)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 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

Structure of LN02-ML85 Fab in complex with DS-SOSIP

Pedenko, B., Effantin, G., Weissenhorn, W., Fenwick, C.

To be published.

Macromolecule Content

Total Structure Weight: 283.05 kDa
Atom Count: 15,933
Modeled Residue Count: 1,866
Deposited Residue Count: 2,364
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A, C, E	481	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 16	Glycosylation Focus chain A Focus chain C Focus chain E
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	B, D, F	161	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B Focus chain D Focus chain F
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain Fab of antibody LN02-ML85	G [auth H]	224	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of antibody LN02-ML85	H [auth L]	214	Homo sapiens	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: 5
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], GA [auth g], BA [auth b], CA [auth c], DA [auth d], EA [auth e], GA [auth g], HA [auth h], I [auth G], IA [auth i], J [auth I], JA [auth j], K [auth J], L [auth K], 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 GA [auth g] Focus chain HA [auth h] Focus chain I [auth G] Focus chain IA [auth i] Focus chain J [auth I] Focus chain JA [auth j] Focus chain K [auth J] Focus chain L [auth K] 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 GA [auth g] Focus chain HA [auth h] Focus chain I [auth G] Focus chain IA [auth i] Focus chain J [auth I] Focus chain JA [auth j] Focus chain K [auth J] Focus chain L [auth K] 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

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	Q	5		N-Glycosylation	Interactions Focus chain Q Interactions & Density Focus chain Q
Glycosylation Resources
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK

Entity ID: 7
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]	5		N-Glycosylation	Interactions Focus chain AA [auth a] Interactions & Density Focus chain AA [auth a]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 8
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)-2-acetamido-2-deoxy-beta-D-glucopyranose	FA [auth f]	4		N-Glycosylation	Interactions Focus chain FA [auth f] Interactions & Density Focus chain FA [auth f]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain ZA [auth C] SDF format, chain YA [auth C] SDF format, chain XA [auth C] SDF format, chain WA [auth C] SDF format, chain VA [auth C] SDF format, chain UA [auth C] SDF format, chain TA [auth C] SDF format, chain SA [auth B] SDF format, chain RA [auth B] SDF format, chain QA [auth B] SDF format, chain PA [auth B] SDF format, chain OA [auth A] SDF format, chain NA [auth A] SDF format, chain MB [auth F] SDF format, chain MA [auth A] SDF format, chain LB [auth F] SDF format, chain LA [auth A] SDF format, chain KB [auth E] SDF format, chain KA [auth A] SDF format, chain JB [auth E] SDF format, chain IB [auth E] SDF format, chain HB [auth E] SDF format, chain GB [auth E] SDF format, chain FB [auth E] SDF format, chain EB [auth E] SDF format, chain DB [auth E] SDF format, chain CB [auth E] SDF format, chain BB [auth D] SDF format, chain AB [auth D] MOL2 format, chain ZA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain SA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain OA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain MB [auth F] MOL2 format, chain MA [auth A] MOL2 format, chain LB [auth F] MOL2 format, chain LA [auth A] MOL2 format, chain KB [auth E] MOL2 format, chain KA [auth A] MOL2 format, chain JB [auth E] MOL2 format, chain IB [auth E] MOL2 format, chain HB [auth E] MOL2 format, chain GB [auth E] MOL2 format, chain FB [auth E] MOL2 format, chain EB [auth E] MOL2 format, chain DB [auth E] MOL2 format, chain CB [auth E] MOL2 format, chain BB [auth D] MOL2 format, chain AB [auth D] mmCIF format, chain ZA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain SA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain OA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain MB [auth F] mmCIF format, chain MA [auth A] mmCIF format, chain LB [auth F] mmCIF format, chain LA [auth A] mmCIF format, chain KB [auth E] mmCIF format, chain KA [auth A] mmCIF format, chain JB [auth E] mmCIF format, chain IB [auth E] mmCIF format, chain HB [auth E] mmCIF format, chain GB [auth E] mmCIF format, chain FB [auth E] mmCIF format, chain EB [auth E] mmCIF format, chain DB [auth E] mmCIF format, chain CB [auth E] mmCIF format, chain BB [auth D] mmCIF format, chain AB [auth D]	AB [auth D] BB [auth D] CB [auth E] DB [auth E] EB [auth E] AB [auth D], BB [auth D], CB [auth E], DB [auth E], EB [auth E], FB [auth E], GB [auth E], HB [auth E], IB [auth E], JB [auth E], KA [auth A], KB [auth E], LA [auth A], LB [auth F], MA [auth A], MB [auth F], NA [auth A], OA [auth A], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth C], UA [auth C], VA [auth C], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EB [auth E] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HB [auth E] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain KA [auth A] Focus chain KB [auth E] Focus chain LA [auth A] Focus chain LB [auth F] Focus chain MA [auth A] Focus chain MB [auth F] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EB [auth E] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HB [auth E] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain KA [auth A] Focus chain KB [auth E] Focus chain LA [auth A] Focus chain LB [auth F] Focus chain MA [auth A] Focus chain MB [auth F] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]