6BF4

Crystal Structure of HIV-1 Clade AE Strain CNE55 gp120 Core in Complex with Neutralizing Antibody VRC-PG05 that Targets the Center of the Silent Face on the Outer Domain of gp120

PDB DOI: https://doi.org/10.2210/pdb6BF4/pdb

Classification: viral protein/immune system
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2017-10-25 Released: 2018-03-07
Deposition Author(s): Zhou, T., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.228
R-Value Work: 0.192
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 188.01 kDa
Atom Count: 13,124
Modelled Residue Count: 1,553
Deposited Residue Count: 1,584
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 clade AE gp120 core	A, D [auth G]	344	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for D7S2G1 (Human immunodeficiency virus 1) Explore D7S2G1 Go to UniProtKB: D7S2G1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D7S2G1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC-PG05 Fab heavy chain	B, E [auth H]	229	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC-PG05 Fab light chain	C, F [auth L]	219	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: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth D]	10		N-Glycosylation	Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]
Glycosylation Resources
GlyTouCan: G12406PI GlyCosmos: G12406PI GlyGen: G12406PI

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	H [auth E]	2		N-Glycosylation	Interactions Focus chain H [auth E] Interactions & Density Focus chain H [auth E]
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)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth F]	6		N-Glycosylation	Interactions Focus chain I [auth F] Interactions & Density Focus chain I [auth F]
Glycosylation Resources
GlyTouCan: G36544AC GlyCosmos: G36544AC GlyGen: G36544AC

Entity ID: 7
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-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth I], N	9		N-Glycosylation	Interactions Focus chain J [auth I] Focus chain N Interactions & Density Focus chain J [auth I] Focus chain N
Glycosylation Resources
GlyTouCan: G95416NX GlyCosmos: G95416NX GlyGen: G95416NX

Entity ID: 8
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-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth J]	11		N-Glycosylation	Interactions Focus chain K [auth J] Interactions & Density Focus chain K [auth J]
Glycosylation Resources
GlyTouCan: G13847GJ GlyCosmos: G13847GJ GlyGen: G13847GJ

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth K]	5		N-Glycosylation	Interactions Focus chain L [auth K] Interactions & Density Focus chain L [auth K]
Glycosylation Resources
GlyTouCan: G21381MC GlyCosmos: G21381MC GlyGen: G21381MC

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M	5		N-Glycosylation	Interactions Focus chain M Interactions & Density Focus chain M
Glycosylation Resources
GlyTouCan: G75436UI GlyCosmos: G75436UI GlyGen: G75436UI

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain DA [auth G] SDF format, chain EA [auth G] SDF format, chain O [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain Y [auth C] SDF format, chain CA [auth G] SDF format, chain HA [auth L] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain Z [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain CA [auth G] MOL2 format, chain HA [auth L] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain Z [auth G]	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], HA [auth L], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], Y [auth C], Z [auth G]	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 HA [auth L] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain Y [auth C] Focus chain Z [auth G] 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 HA [auth L] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain Y [auth C] Focus chain Z [auth G]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain FA [auth G] SDF format, chain GA [auth H] SDF format, chain IA [auth L] SDF format, chain JA [auth L] SDF format, chain U [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain IA [auth L] MOL2 format, chain JA [auth L] MOL2 format, chain U [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	FA [auth G] GA [auth H] IA [auth L] JA [auth L] U [auth A] FA [auth G], GA [auth H], IA [auth L], JA [auth L], U [auth A], V [auth B], W [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FA [auth G] Focus chain GA [auth H] Focus chain IA [auth L] Focus chain JA [auth L] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain FA [auth G] Focus chain GA [auth H] Focus chain IA [auth L] Focus chain JA [auth L] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B]	X [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain X [auth B] Interactions & Density Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.228
R-Value Work: 0.192
R-Value Observed: 0.194
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 231.438	α = 90
b = 89.255	β = 119.15
c = 123.407	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-03-07

Deposition Author(s):

Zhou, T.

Kwong, P.D.

Revision History (Full details and data files)

Version 1.0: 2018-03-07
Type: Initial release
Version 1.1: 2018-04-18
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary