5U7M

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-378806 in Complex with Human Antibodies PGT122 and 35O22 at 3.8 Angstrom

PDB DOI: https://doi.org/10.2210/pdb5U7M/pdb

Classification: VIRAL PROTEIN/Immune system
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2016-12-12 Released: 2017-08-30
Deposition Author(s): Pancera, M., Lai, Y.-T., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.02 Å
R-Value Free: 0.289
R-Value Work: 0.245
R-Value Observed: 0.248

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 180.98 kDa
Atom Count: 12,026
Modelled Residue Count: 1,459
Deposited Residue Count: 1,541
Unique protein chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A [auth B]	153	Human immunodeficiency virus 1	Mutation(s): 2 Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus 1) Explore Q2N0S5 Go to UniProtKB: Q2N0S5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22 FAB HEAVY CHAIN	B [auth D]	243	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22 FAB LIGHT CHAIN	C [auth E]	216	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	D [auth G]	481	Human immunodeficiency virus 1	Mutation(s): 6 Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus 1) Explore Q2N0S5 Go to UniProtKB: Q2N0S5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S5
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT122 FAB HEAVY CHAIN	E [auth H]	235	Homo sapiens	Mutation(s): 0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT122 FAB LIGHT CHAIN	F [auth L]	213	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: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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	G [auth A]	7		N-Glycosylation	Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth C], S	3		N-Glycosylation	Interactions Focus chain H [auth C] Focus chain S Interactions & Density Focus chain H [auth C] Focus chain S
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 9
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	I [auth F]	5		N-Glycosylation	Interactions Focus chain I [auth F] Interactions & Density Focus chain I [auth F]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth I], K [auth J], M, N, P, J [auth I], K [auth J], M, N, P, Q, R	2		N-Glycosylation	Interactions Focus chain J [auth I] Focus chain K [auth J] Focus chain M Focus chain N Focus chain P Focus chain Q Focus chain R Interactions & Density Focus chain J [auth I] Focus chain K [auth J] Focus chain M Focus chain N Focus chain P Focus chain Q Focus chain R
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-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	L [auth K]	6		N-Glycosylation	Interactions Focus chain L [auth K] Interactions & Density Focus chain L [auth K]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 12
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	O	10		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G91704UR GlyCosmos: G91704UR GlyGen: G91704UR

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
83G Query on 83G Download Ideal Coordinates CCD File SDF format, chain FA [auth G] MOL2 format, chain FA [auth G]	FA [auth G]	1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione C₂₂ H₂₂ N₄ O₄ OKGPFTLYBPQBIX-CQSZACIVSA-N		Interactions Focus chain FA [auth G] Interactions & Density Focus chain FA [auth G]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain DA [auth G] SDF format, chain EA [auth G] SDF format, chain AA [auth G] SDF format, chain CA [auth G] SDF format, chain GA [auth H] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain BA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	AA [auth G] BA [auth G] CA [auth G] DA [auth G] EA [auth G] AA [auth G], BA [auth G], CA [auth G], DA [auth G], EA [auth G], GA [auth H], U [auth B], V [auth B], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain GA [auth H] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain GA [auth H] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain HA [auth L] SDF format, chain T [auth B] SDF format, chain X [auth G] SDF format, chain Y [auth G] SDF format, chain Z [auth G] MOL2 format, chain HA [auth L] MOL2 format, chain T [auth B] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth G]	HA [auth L], T [auth B], X [auth G], Y [auth G], Z [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain HA [auth L] Focus chain T [auth B] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain HA [auth L] Focus chain T [auth B] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G]

Binding Affinity Annotations
ID	Source	Binding Affinity
83G	BindingDB: 5U7M	IC50: min: 14, max: 56 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.02 Å
R-Value Free: 0.289
R-Value Work: 0.245
R-Value Observed: 0.248
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.195	α = 90
b = 129.195	β = 90
c = 312.081	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-08-30

Deposition Author(s):

Pancera, M.

Lai, Y.-T.

Kwong, P.D.

Revision History (Full details and data files)

Version 1.0: 2017-08-30
Type: Initial release
Version 1.1: 2017-09-06
Changes: Database references
Version 1.2: 2017-09-20
Changes: Structure summary
Version 1.3: 2017-09-27
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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5U7M

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-378806 in Complex with Human Antibodies PGT122 and 35O22 at 3.8 Angstrom

Entity ID: 1

UniProt

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Sequence Annotations

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Entity ID: 2

Entity Groups

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Entity ID: 3

Entity Groups

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Entity ID: 4

UniProt

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Sequence Annotations

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Entity ID: 5

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Entity ID: 6

Entity Groups

Sequence Annotations

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Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Entity ID: 11

Glycosylation Resources

Entity ID: 12

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)