5U7O
Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-626529 in Complex with Human Antibodies PGT122 and 35O22 at 3.8 Angstrom
- PDB DOI: https://doi.org/10.2210/pdb5U7O/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 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.03 Å
- R-Value Free: 0.325 
- R-Value Work: 0.272 
- R-Value Observed: 0.275 
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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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 AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
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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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(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
35O22 FAB LIGHT CHAIN | C [auth E] | 216 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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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 | ||||
Sequence AnnotationsExpand | |||||
|
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(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
PGT122 FAB HEAVY CHAIN | E [auth H] | 235 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
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(by identity cutoff) | 3D Structure
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 AnnotationsExpand | |||||
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Oligosaccharides
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 | ||
Glycosylation Resources | |||||
GlyTouCan:  G55220VL GlyCosmos:  G55220VL GlyGen:  G55220VL |
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 | H [auth C] | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
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 | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Entity ID: 10 | |||||
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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], L [auth K], N, O, J [auth I], K [auth J], L [auth K], N, O, Q, R, S | 2 | N-Glycosylation | ||
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 | M | 6 | N-Glycosylation | ||
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 | P | 10 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G91704UR GlyCosmos:  G91704UR GlyGen:  G91704UR |
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
83J Query on 83J | FA [auth G] | 1-[4-(benzenecarbonyl)piperazin-1-yl]-2-[4-methoxy-7-(3-methyl-1H-1,2,4-triazol-1-yl)-1H-pyrrolo[2,3-c]pyridin-3-yl]ethane-1,2-dione C24 H23 N7 O4 QRPZBKAMSFHVRW-UHFFFAOYSA-N | |||
NAG Query on NAG | BA [auth G] CA [auth G] DA [auth G] EA [auth G] GA [auth H] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | AA [auth G], HA [auth L], U [auth B], Y [auth G], Z [auth G] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.03 Å
- R-Value Free: 0.325 
- R-Value Work: 0.272 
- R-Value Observed: 0.275 
- Space Group: P 63
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 131.027 | α = 90 |
b = 131.027 | β = 90 |
c = 311.491 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
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 1.4: 2017-10-18
Changes: Structure summary - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary