5WDU

HIV-1 Env BG505 SOSIP.664 H72C-H564C trimer in complex with bNAbs PGT122 Fab, 35O22 Fab and NIH45-46 scFv

PDB DOI: https://doi.org/10.2210/pdb5WDU/pdb

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

Deposited: 2017-07-06 Released: 2018-04-04
Deposition Author(s): Julien, J.-P., Torrents de la Pena, A., Sanders, R.W., Wilson, I.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), International AIDS Vaccine Initiative

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 7.00 Å
R-Value Free: 0.363
R-Value Work: 0.301
R-Value Observed: 0.304

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 4.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 612.66 kDa
Atom Count: 41,285
Modelled Residue Count: 5,066
Deposited Residue Count: 5,295
Unique protein chains: 7

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A [auth G], C [auth F], E [auth Q]	471	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
bnAb NIH45-46 scFv	B [auth D], D [auth O], F [auth W]	250	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	G [auth A], L [auth J], Q [auth R]	147	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
bnAb PGT122 Fab light chain	H [auth B], M [auth K], R [auth S]	210	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
bnAb PGT122 Fab heavy chain	I [auth C], N [auth L], S [auth T]	232	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
bnAb 35O22 Fab heavy chain	J [auth H], O [auth M], T [auth U]	242	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: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
bnAb 35O22 Fab light chain	K [auth I], P [auth N], U [auth V]	213	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

Oligosaccharides

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Entity ID: 8
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	CA [auth c], EA [auth e], GA [auth g], LA [auth l], NA [auth n], CA [auth c], EA [auth e], GA [auth g], LA [auth l], NA [auth n], PA [auth p], UA [auth u], V [auth E], X	5		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain PA [auth p] Focus chain UA [auth u] Focus chain V [auth E] Focus chain X Interactions & Density Focus chain CA [auth c] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain PA [auth p] Focus chain UA [auth u] Focus chain V [auth E] Focus chain X
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 9
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	FA [auth f], OA [auth o], W [auth P]	3		N-Glycosylation	Interactions Focus chain FA [auth f] Focus chain OA [auth o] Focus chain W [auth P] Interactions & Density Focus chain FA [auth f] Focus chain OA [auth o] Focus chain W [auth P]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	HA [auth h], QA [auth q], Y	4		N-Glycosylation	Interactions Focus chain HA [auth h] Focus chain QA [auth q] Focus chain Y Interactions & Density Focus chain HA [auth h] Focus chain QA [auth q] Focus chain Y
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 11
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	IA [auth i], RA [auth r], Z	7		N-Glycosylation	Interactions Focus chain IA [auth i] Focus chain RA [auth r] Focus chain Z Interactions & Density Focus chain IA [auth i] Focus chain RA [auth r] Focus chain Z
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 12
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	AA [auth a], JA [auth j], SA [auth s]	6		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain JA [auth j] Focus chain SA [auth s] Interactions & Density Focus chain AA [auth a] Focus chain JA [auth j] Focus chain SA [auth s]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 13
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], KA [auth k], TA [auth t]	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain KA [auth k] Focus chain TA [auth t] Interactions & Density Focus chain BA [auth b] Focus chain KA [auth k] Focus chain TA [auth t]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 14
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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	DA [auth d], MA [auth m], VA [auth v]	8		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain MA [auth m] Focus chain VA [auth v] Interactions & Density Focus chain DA [auth d] Focus chain MA [auth m] Focus chain VA [auth v]
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

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 BB [auth G] SDF format, chain BC [auth R] SDF format, chain CC [auth R] SDF format, chain DB [auth G] SDF format, chain HB [auth F] SDF format, chain JB [auth F] SDF format, chain KB [auth F] SDF format, chain NB [auth Q] SDF format, chain OB [auth Q] SDF format, chain SB [auth Q] SDF format, chain TB [auth Q] SDF format, chain VB [auth A] SDF format, chain WB [auth A] SDF format, chain YA [auth G] SDF format, chain YB [auth J] SDF format, chain AB [auth G] SDF format, chain AC [auth R] SDF format, chain CB [auth G] SDF format, chain EB [auth F] SDF format, chain FB [auth F] SDF format, chain GB [auth F] SDF format, chain IB [auth F] SDF format, chain LB [auth F] SDF format, chain MB [auth Q] SDF format, chain PB [auth Q] SDF format, chain QB [auth Q] SDF format, chain RB [auth Q] SDF format, chain UB [auth A] SDF format, chain WA [auth G] SDF format, chain XA [auth G] SDF format, chain XB [auth J] SDF format, chain ZA [auth G] SDF format, chain ZB [auth J] MOL2 format, chain BB [auth G] MOL2 format, chain BC [auth R] MOL2 format, chain CC [auth R] MOL2 format, chain DB [auth G] MOL2 format, chain HB [auth F] MOL2 format, chain JB [auth F] MOL2 format, chain KB [auth F] MOL2 format, chain NB [auth Q] MOL2 format, chain OB [auth Q] MOL2 format, chain SB [auth Q] MOL2 format, chain TB [auth Q] MOL2 format, chain VB [auth A] MOL2 format, chain WB [auth A] MOL2 format, chain YA [auth G] MOL2 format, chain YB [auth J] MOL2 format, chain AB [auth G] MOL2 format, chain AC [auth R] MOL2 format, chain CB [auth G] MOL2 format, chain EB [auth F] MOL2 format, chain FB [auth F] MOL2 format, chain GB [auth F] MOL2 format, chain IB [auth F] MOL2 format, chain LB [auth F] MOL2 format, chain MB [auth Q] MOL2 format, chain PB [auth Q] MOL2 format, chain QB [auth Q] MOL2 format, chain RB [auth Q] MOL2 format, chain UB [auth A] MOL2 format, chain WA [auth G] MOL2 format, chain XA [auth G] MOL2 format, chain XB [auth J] MOL2 format, chain ZA [auth G] MOL2 format, chain ZB [auth J]	AB [auth G] AC [auth R] BB [auth G] BC [auth R] CB [auth G] AB [auth G], AC [auth R], BB [auth G], BC [auth R], CB [auth G], CC [auth R], DB [auth G], EB [auth F], FB [auth F], GB [auth F], HB [auth F], IB [auth F], JB [auth F], KB [auth F], LB [auth F], MB [auth Q], NB [auth Q], OB [auth Q], PB [auth Q], QB [auth Q], RB [auth Q], SB [auth Q], TB [auth Q], UB [auth A], VB [auth A], WA [auth G], WB [auth A], XA [auth G], XB [auth J], YA [auth G], YB [auth J], ZA [auth G], ZB [auth J]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth G] Focus chain AC [auth R] Focus chain BB [auth G] Focus chain BC [auth R] Focus chain CB [auth G] Focus chain CC [auth R] Focus chain DB [auth G] Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain IB [auth F] Focus chain JB [auth F] Focus chain KB [auth F] Focus chain LB [auth F] Focus chain MB [auth Q] Focus chain NB [auth Q] Focus chain OB [auth Q] Focus chain PB [auth Q] Focus chain QB [auth Q] Focus chain RB [auth Q] Focus chain SB [auth Q] Focus chain TB [auth Q] Focus chain UB [auth A] Focus chain VB [auth A] Focus chain WA [auth G] Focus chain WB [auth A] Focus chain XA [auth G] Focus chain XB [auth J] Focus chain YA [auth G] Focus chain YB [auth J] Focus chain ZA [auth G] Focus chain ZB [auth J] Interactions & Density Focus chain AB [auth G] Focus chain AC [auth R] Focus chain BB [auth G] Focus chain BC [auth R] Focus chain CB [auth G] Focus chain CC [auth R] Focus chain DB [auth G] Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain IB [auth F] Focus chain JB [auth F] Focus chain KB [auth F] Focus chain LB [auth F] Focus chain MB [auth Q] Focus chain NB [auth Q] Focus chain OB [auth Q] Focus chain PB [auth Q] Focus chain QB [auth Q] Focus chain RB [auth Q] Focus chain SB [auth Q] Focus chain TB [auth Q] Focus chain UB [auth A] Focus chain VB [auth A] Focus chain WA [auth G] Focus chain WB [auth A] Focus chain XA [auth G] Focus chain XB [auth J] Focus chain YA [auth G] Focus chain YB [auth J] Focus chain ZA [auth G] Focus chain ZB [auth J]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	B [auth D], D [auth O], F [auth W]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 7.00 Å
R-Value Free: 0.363
R-Value Work: 0.301
R-Value Observed: 0.304
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 361.81	α = 90
b = 215.85	β = 114.03
c = 176.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-04-04

Deposition Author(s):

Julien, J.-P.

Torrents de la Pena, A.

Sanders, R.W.

Wilson, I.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI110657
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	Scripps CHAVI-ID UM1 AI100663
International AIDS Vaccine Initiative	United States	IAVI

Revision History (Full details and data files)

Version 1.0: 2018-04-04
Type: Initial release
Version 1.1: 2019-02-20
Changes: Author supporting evidence, Data collection
Version 2.0: 2019-12-11
Changes: Author supporting evidence, Polymer sequence
Version 3.0: 2020-01-01
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
Version 4.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 4.1: 2022-11-30
Changes: Database references, Derived calculations, Structure summary

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5WDU

HIV-1 Env BG505 SOSIP.664 H72C-H564C trimer in complex with bNAbs PGT122 Fab, 35O22 Fab and NIH45-46 scFv

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

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Entity ID: 4

Entity Groups

Sequence Annotations

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Entity ID: 5

Entity Groups

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Entity ID: 6

Entity Groups

Sequence Annotations

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Entity ID: 7

Entity Groups

Sequence Annotations

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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

Entity ID: 13

Glycosylation Resources

Entity ID: 14

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)