7TJO | pdb_00007tjo

HIV-1 gp120 complex with CJF-II-197-S

PDB DOI: https://doi.org/10.2210/pdb7TJO/pdb

Classification: VIRUS
Organism(s): HIV-1 06TG.HT008
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-01-16 Released: 2023-01-25
Deposition Author(s): Gong, Z., Hendrickson, W.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.07 Å
R-Value Free:
0.268 (Depositor), 0.270 (DCC)
R-Value Work:
0.229 (Depositor), 0.229 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural and Functional Characterization of Indane-Core CD4-Mimetic Compounds Substituted with Heterocyclic Amines

Chaplain, C., Fritschi, C.J., Anang, S., Gong, Z., Richard, J., Bourassa, C., Liang, S., Mohammadi, M., Park, J., Finzi, A., Madani, N., Sodroski, J.G., Abrams, C.F., Hendrickson, W.A., Smith, A.B.

(2023) ACS Med Chem Lett 14: 51-58

DOI: https://doi.org/10.1021/acsmedchemlett.2c00376

Macromolecule Content

Total Structure Weight: 169.06 kDa
Atom Count: 11,224
Modeled Residue Count: 1,340
Deposited Residue Count: 1,432
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein 120	A [auth D], B [auth A], C, D [auth B]	358	HIV-1 06TG.HT008	Mutation(s): 0
UniProt
Find proteins for A0ACD6BAG2 (Simian-Human immunodeficiency virus) Explore A0ACD6BAG2 Go to UniProtKB: A0ACD6BAG2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BAG2
Glycosylation
Glycosylation Sites: 9	Glycosylation Focus chain A [auth D] Focus chain B [auth A] Focus chain C Focus chain D [auth B]
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I6Q Query on I6Q Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain O [auth A] SDF format, chain JA [auth B] SDF format, chain E [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain O [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain E [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain O [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain E [auth D]	E [auth D], JA [auth B], O [auth A], Z [auth C]	N~1~-[(1R,2R)-5-{[(3R)-3-aminopyrrolidin-1-yl]methyl}-2-(carbamimidamidomethyl)-2,3-dihydro-1H-inden-1-yl]-N~2~-(4-chloro-3-fluorophenyl)ethanediamide C₂₄ H₂₉ Cl F N₇ O₂ UJGBLAVDKVSVBC-WHSLLNHNSA-N		Interactions Focus chain E [auth D] Focus chain JA [auth B] Focus chain O [auth A] Focus chain Z [auth C] Interactions & Density Focus chain E [auth D] Focus chain JA [auth B] Focus chain O [auth A] Focus chain Z [auth C]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain L [auth D] SDF format, chain N [auth D] SDF format, chain OA [auth B] SDF format, chain U [auth A] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain T [auth A] SDF format, chain SA [auth B] SDF format, chain S [auth A] SDF format, chain RA [auth B] SDF format, chain R [auth A] SDF format, chain QA [auth B] SDF format, chain Q [auth A] SDF format, chain PA [auth B] SDF format, chain P [auth A] SDF format, chain NA [auth B] SDF format, chain MA [auth B] SDF format, chain M [auth D] SDF format, chain LA [auth B] SDF format, chain KA [auth B] SDF format, chain K [auth D] SDF format, chain J [auth D] SDF format, chain IA [auth C] SDF format, chain I [auth D] SDF format, chain HA [auth C] SDF format, chain GA [auth C] SDF format, chain G [auth D] SDF format, chain FA [auth C] SDF format, chain F [auth D] SDF format, chain EA [auth C] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain H [auth D] MOL2 format, chain L [auth D] MOL2 format, chain N [auth D] MOL2 format, chain OA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth D] MOL2 format, chain LA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] MOL2 format, chain IA [auth C] MOL2 format, chain I [auth D] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain G [auth D] MOL2 format, chain FA [auth C] MOL2 format, chain F [auth D] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain H [auth D] mmCIF format, chain L [auth D] mmCIF format, chain N [auth D] mmCIF format, chain OA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth D] mmCIF format, chain LA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D] mmCIF format, chain IA [auth C] mmCIF format, chain I [auth D] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain G [auth D] mmCIF format, chain FA [auth C] mmCIF format, chain F [auth D] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] EA [auth C] AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], F [auth D], FA [auth C], G [auth D], GA [auth C], H [auth D], HA [auth C], I [auth D], IA [auth C], J [auth D], K [auth D], KA [auth B], L [auth D], LA [auth B], M [auth D], MA [auth B], N [auth D], NA [auth B], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth D] Focus chain FA [auth C] Focus chain G [auth D] Focus chain GA [auth C] Focus chain H [auth D] Focus chain HA [auth C] Focus chain I [auth D] Focus chain IA [auth C] Focus chain J [auth D] Focus chain K [auth D] Focus chain KA [auth B] Focus chain L [auth D] Focus chain LA [auth B] Focus chain M [auth D] Focus chain MA [auth B] Focus chain N [auth D] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth D] Focus chain FA [auth C] Focus chain G [auth D] Focus chain GA [auth C] Focus chain H [auth D] Focus chain HA [auth C] Focus chain I [auth D] Focus chain IA [auth C] Focus chain J [auth D] Focus chain K [auth D] Focus chain KA [auth B] Focus chain L [auth D] Focus chain LA [auth B] Focus chain M [auth D] Focus chain MA [auth B] Focus chain N [auth D] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain Y [auth A]	Y [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain Y [auth A] Interactions & Density Focus chain Y [auth A]