4YDK

Crystal structure of broadly and potently neutralizing antibody C38-VRC16.01 in complex with HIV-1 clade AE strain 93TH057 gp120

PDB DOI: https://doi.org/10.2210/pdb4YDK/pdb

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

Deposited: 2015-02-22 Released: 2015-06-03
Deposition Author(s): Zhou, T., Moquin, S., Zheng, A., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.206
R-Value Work: 0.166
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 92.27 kDa
Atom Count: 6,813
Modelled Residue Count: 785
Deposited Residue Count: 801
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,Envelope glycoprotein gp160	A [auth G]	353	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
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
HEAVY CHAIN OF ANTIBODY C38-VRC16.01	B [auth H]	234	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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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LIGHT CHAIN OF ANTIBODY C38-VRC16.01	C [auth L]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth G] SDF format, chain E [auth G] SDF format, chain F [auth G] SDF format, chain G SDF format, chain H [auth G] SDF format, chain I [auth G] SDF format, chain J [auth G] SDF format, chain K [auth G] SDF format, chain L [auth G] SDF format, chain M [auth G] MOL2 format, chain D [auth G] MOL2 format, chain E [auth G] MOL2 format, chain F [auth G] MOL2 format, chain G MOL2 format, chain H [auth G] MOL2 format, chain I [auth G] MOL2 format, chain J [auth G] MOL2 format, chain K [auth G] MOL2 format, chain L [auth G] MOL2 format, chain M [auth G]	D [auth G] E [auth G] F [auth G] G H [auth G] D [auth G], E [auth G], F [auth G], G, H [auth G], I [auth G], J [auth G], K [auth G], L [auth G], M [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth G] Focus chain E [auth G] Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain I [auth G] Focus chain J [auth G] Focus chain K [auth G] Focus chain L [auth G] Focus chain M [auth G] Interactions & Density Focus chain D [auth G] Focus chain E [auth G] Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain I [auth G] Focus chain J [auth G] Focus chain K [auth G] Focus chain L [auth G] Focus chain M [auth G]
NHE Query on NHE Download Ideal Coordinates CCD File SDF format, chain S [auth G] MOL2 format, chain S [auth G]	S [auth G]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain S [auth G] Interactions & Density Focus chain S [auth G]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain BA [auth L] SDF format, chain CA [auth L] SDF format, chain N [auth G] SDF format, chain O [auth G] SDF format, chain P [auth G] SDF format, chain Q [auth G] SDF format, chain X [auth H] MOL2 format, chain BA [auth L] MOL2 format, chain CA [auth L] MOL2 format, chain N [auth G] MOL2 format, chain O [auth G] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain X [auth H]	BA [auth L] CA [auth L] N [auth G] O [auth G] P [auth G] BA [auth L], CA [auth L], N [auth G], O [auth G], P [auth G], Q [auth G], X [auth H]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth L] Focus chain CA [auth L] Focus chain N [auth G] Focus chain O [auth G] Focus chain P [auth G] Focus chain Q [auth G] Focus chain X [auth H] Interactions & Density Focus chain BA [auth L] Focus chain CA [auth L] Focus chain N [auth G] Focus chain O [auth G] Focus chain P [auth G] Focus chain Q [auth G] Focus chain X [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain DA [auth L] SDF format, chain EA [auth L] SDF format, chain FA [auth L] SDF format, chain GA [auth L] SDF format, chain HA [auth L] SDF format, chain R [auth G] SDF format, chain T [auth G] SDF format, chain U [auth G] SDF format, chain V [auth G] SDF format, chain W [auth G] SDF format, chain Y [auth H] SDF format, chain Z [auth H] MOL2 format, chain AA [auth H] MOL2 format, chain DA [auth L] MOL2 format, chain EA [auth L] MOL2 format, chain FA [auth L] MOL2 format, chain GA [auth L] MOL2 format, chain HA [auth L] MOL2 format, chain R [auth G] MOL2 format, chain T [auth G] MOL2 format, chain U [auth G] MOL2 format, chain V [auth G] MOL2 format, chain W [auth G] MOL2 format, chain Y [auth H] MOL2 format, chain Z [auth H]	AA [auth H] DA [auth L] EA [auth L] FA [auth L] GA [auth L] AA [auth H], DA [auth L], EA [auth L], FA [auth L], GA [auth L], HA [auth L], R [auth G], T [auth G], U [auth G], V [auth G], W [auth G], Y [auth H], Z [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain DA [auth L] Focus chain EA [auth L] Focus chain FA [auth L] Focus chain GA [auth L] Focus chain HA [auth L] Focus chain R [auth G] Focus chain T [auth G] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain Y [auth H] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth H] Focus chain DA [auth L] Focus chain EA [auth L] Focus chain FA [auth L] Focus chain GA [auth L] Focus chain HA [auth L] Focus chain R [auth G] Focus chain T [auth G] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain Y [auth H] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.206
R-Value Work: 0.166
R-Value Observed: 0.168
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.836	α = 90
b = 109.686	β = 126.26
c = 100.063	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-06-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-06-03
Type: Initial release
Version 1.1: 2015-06-10
Changes: Database references
Version 1.2: 2015-06-17
Changes: Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Source and taxonomy, Structure summary
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary