3NGB

Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 gp120

PDB DOI: https://doi.org/10.2210/pdb3NGB/pdb

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

Deposited: 2010-06-11 Released: 2010-07-07
Deposition Author(s): Zhou, T., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.256
R-Value Work: 0.197
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 363.54 kDa
Atom Count: 25,808
Modelled Residue Count: 3,127
Deposited Residue Count: 3,148
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A [auth G], D [auth A], G [auth D], J [auth I]	353	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: Env, pol
UniProt
Find proteins for Q0ED31 (Human immunodeficiency virus 1) Explore Q0ED31 Go to UniProtKB: Q0ED31
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0ED31
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen binding fragment of heavy chain: Antibody VRC01	B [auth H], E [auth B], H [auth E], K [auth J]	224	Homo sapiens	Mutation(s): 0 Gene Names: Heavy chain
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
Antigen binding fragment of light chain: Antibody VRC01	C [auth L], F [auth C], I [auth F], L [auth K]	210	Homo sapiens	Mutation(s): 0 Gene Names: Light chain
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-(1-3)-[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, N, P	5		N-Glycosylation	Interactions Focus chain M Focus chain N Focus chain P Interactions & Density Focus chain M Focus chain N Focus chain P
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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	O	2		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 AB [auth D] SDF format, chain BB [auth D] SDF format, chain CA [auth A] SDF format, chain CB [auth D] SDF format, chain DA [auth A] SDF format, chain DB [auth D] SDF format, chain EA [auth A] SDF format, chain EB [auth D] SDF format, chain FA [auth A] SDF format, chain FB [auth D] SDF format, chain GA [auth A] SDF format, chain GB [auth D] SDF format, chain HA [auth A] SDF format, chain HB [auth D] SDF format, chain IA [auth A] SDF format, chain IB [auth D] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain NB [auth I] SDF format, chain OB [auth I] SDF format, chain PB [auth I] SDF format, chain Q [auth G] SDF format, chain QB [auth I] SDF format, chain R [auth G] SDF format, chain RB [auth I] SDF format, chain S [auth G] SDF format, chain SB [auth I] SDF format, chain T [auth G] SDF format, chain TB [auth I] SDF format, chain U [auth G] SDF format, chain UB [auth I] SDF format, chain V [auth G] SDF format, chain VB [auth I] SDF format, chain W [auth G] SDF format, chain WB [auth I] SDF format, chain X [auth G] SDF format, chain XA [auth D] SDF format, chain XB [auth I] SDF format, chain Y [auth G] SDF format, chain YA [auth D] SDF format, chain Z [auth G] SDF format, chain ZA [auth D] MOL2 format, chain AA [auth G] MOL2 format, chain AB [auth D] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth D] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth D] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth I] MOL2 format, chain OB [auth I] MOL2 format, chain PB [auth I] MOL2 format, chain Q [auth G] MOL2 format, chain QB [auth I] MOL2 format, chain R [auth G] MOL2 format, chain RB [auth I] MOL2 format, chain S [auth G] MOL2 format, chain SB [auth I] MOL2 format, chain T [auth G] MOL2 format, chain TB [auth I] MOL2 format, chain U [auth G] MOL2 format, chain UB [auth I] MOL2 format, chain V [auth G] MOL2 format, chain VB [auth I] MOL2 format, chain W [auth G] MOL2 format, chain WB [auth I] MOL2 format, chain X [auth G] MOL2 format, chain XA [auth D] MOL2 format, chain XB [auth I] MOL2 format, chain Y [auth G] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth G] MOL2 format, chain ZA [auth D]	AA [auth G] AB [auth D] BB [auth D] CA [auth A] CB [auth D] AA [auth G], AB [auth D], BB [auth D], CA [auth A], CB [auth D], DA [auth A], DB [auth D], EA [auth A], EB [auth D], FA [auth A], FB [auth D], GA [auth A], GB [auth D], HA [auth A], HB [auth D], IA [auth A], IB [auth D], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], NB [auth I], OB [auth I], PB [auth I], Q [auth G], QB [auth I], R [auth G], RB [auth I], S [auth G], SB [auth I], T [auth G], TB [auth I], U [auth G], UB [auth I], V [auth G], VB [auth I], W [auth G], WB [auth I], X [auth G], XA [auth D], XB [auth I], Y [auth G], YA [auth D], Z [auth G], ZA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth G] Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CA [auth A] Focus chain CB [auth D] Focus chain DA [auth A] Focus chain DB [auth D] Focus chain EA [auth A] Focus chain EB [auth D] Focus chain FA [auth A] Focus chain FB [auth D] Focus chain GA [auth A] Focus chain GB [auth D] Focus chain HA [auth A] Focus chain HB [auth D] Focus chain IA [auth A] Focus chain IB [auth D] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain NB [auth I] Focus chain OB [auth I] Focus chain PB [auth I] Focus chain Q [auth G] Focus chain QB [auth I] Focus chain R [auth G] Focus chain RB [auth I] Focus chain S [auth G] Focus chain SB [auth I] Focus chain T [auth G] Focus chain TB [auth I] Focus chain U [auth G] Focus chain UB [auth I] Focus chain V [auth G] Focus chain VB [auth I] Focus chain W [auth G] Focus chain WB [auth I] Focus chain X [auth G] Focus chain XA [auth D] Focus chain XB [auth I] Focus chain Y [auth G] Focus chain YA [auth D] Focus chain Z [auth G] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth G] Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CA [auth A] Focus chain CB [auth D] Focus chain DA [auth A] Focus chain DB [auth D] Focus chain EA [auth A] Focus chain EB [auth D] Focus chain FA [auth A] Focus chain FB [auth D] Focus chain GA [auth A] Focus chain GB [auth D] Focus chain HA [auth A] Focus chain HB [auth D] Focus chain IA [auth A] Focus chain IB [auth D] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain NB [auth I] Focus chain OB [auth I] Focus chain PB [auth I] Focus chain Q [auth G] Focus chain QB [auth I] Focus chain R [auth G] Focus chain RB [auth I] Focus chain S [auth G] Focus chain SB [auth I] Focus chain T [auth G] Focus chain TB [auth I] Focus chain U [auth G] Focus chain UB [auth I] Focus chain V [auth G] Focus chain VB [auth I] Focus chain W [auth G] Focus chain WB [auth I] Focus chain X [auth G] Focus chain XA [auth D] Focus chain XB [auth I] Focus chain Y [auth G] Focus chain YA [auth D] Focus chain Z [auth G] Focus chain ZA [auth D]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain CC [auth J] SDF format, chain LB [auth D] SDF format, chain MB [auth E] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain SA [auth A] SDF format, chain TA [auth A] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain WA [auth C] SDF format, chain YB [auth I] SDF format, chain ZB [auth I] MOL2 format, chain BA [auth G] MOL2 format, chain CC [auth J] MOL2 format, chain LB [auth D] MOL2 format, chain MB [auth E] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain YB [auth I] MOL2 format, chain ZB [auth I]	BA [auth G] CC [auth J] LB [auth D] MB [auth E] QA [auth A] BA [auth G], CC [auth J], LB [auth D], MB [auth E], QA [auth A], RA [auth A], SA [auth A], TA [auth A], UA [auth B], VA [auth B], WA [auth C], YB [auth I], ZB [auth I]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain BA [auth G] Focus chain CC [auth J] Focus chain LB [auth D] Focus chain MB [auth E] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth C] Focus chain YB [auth I] Focus chain ZB [auth I] Interactions & Density Focus chain BA [auth G] Focus chain CC [auth J] Focus chain LB [auth D] Focus chain MB [auth E] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth C] Focus chain YB [auth I] Focus chain ZB [auth I]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain AC [auth I] SDF format, chain BC [auth J] SDF format, chain DC [auth K] SDF format, chain JB [auth D] SDF format, chain KB [auth D] SDF format, chain OA [auth A] SDF format, chain PA [auth A] MOL2 format, chain AC [auth I] MOL2 format, chain BC [auth J] MOL2 format, chain DC [auth K] MOL2 format, chain JB [auth D] MOL2 format, chain KB [auth D] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A]	AC [auth I] BC [auth J] DC [auth K] JB [auth D] KB [auth D] AC [auth I], BC [auth J], DC [auth K], JB [auth D], KB [auth D], OA [auth A], PA [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain AC [auth I] Focus chain BC [auth J] Focus chain DC [auth K] Focus chain JB [auth D] Focus chain KB [auth D] Focus chain OA [auth A] Focus chain PA [auth A] Interactions & Density Focus chain AC [auth I] Focus chain BC [auth J] Focus chain DC [auth K] Focus chain JB [auth D] Focus chain KB [auth D] Focus chain OA [auth A] Focus chain PA [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.256
R-Value Work: 0.197
R-Value Observed: 0.200
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.63	α = 90
b = 98.275	β = 99.68
c = 205.256	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-07-07

Deposition Author(s):

Zhou, T.

Kwong, P.D.

Revision History (Full details and data files)

Version 1.0: 2010-07-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-08-23
Changes: Refinement description, Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 3.0: 2020-10-14
Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
Version 3.1: 2021-03-31
Changes: Source and taxonomy
Version 3.2: 2023-09-06
Changes: Data collection, Database references, Refinement description