7SX6

Crystal structure of broadly neutralizing antibody N49P9.3 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core

PDB DOI: https://doi.org/10.2210/pdb7SX6/pdb

Classification: IMMUNE SYSTEM/VIRAL PROTEIN
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2021-11-22 Released: 2022-11-30
Deposition Author(s): Tolbert, W.D., Pazgier, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.292 (Depositor), 0.292 (DCC)
R-Value Work:
0.240 (Depositor), 0.239 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of broadly neutralizing antibody N49P9.3 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core

Tolbert, W.D., Pazgier, M.

To be published.

Macromolecule Content

Total Structure Weight: 175.45 kDa
Atom Count: 11,995
Modelled Residue Count: 1,516
Deposited Residue Count: 1,562
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
clade A/E 93TH057 HIV-1 gp120 core	A [auth G], D [auth A]	355	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: HIV-1 Env
UniProt
Find proteins for A0A0M3KKW9 (Human immunodeficiency virus type 1) Explore A0A0M3KKW9 Go to UniProtKB: A0A0M3KKW9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0M3KKW9
Glycosylation
Glycosylation Sites: 10	Glycosylation Focus chain A [auth G] Focus chain D [auth A]
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N49P9.3 ANTIBODY FAB HEAVY CHAIN	B [auth H], E [auth B]	223	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N49P9.3 ANTIBODY FAB LIGHT CHAIN	C [auth L], F [auth C]	203	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

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 A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] 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] SDF format, chain N [auth G] SDF format, chain O [auth G] SDF format, chain P [auth G] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] 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] MOL2 format, chain N [auth G] MOL2 format, chain O [auth G] MOL2 format, chain P [auth G] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain G mmCIF format, chain H [auth G] mmCIF format, chain I [auth G] mmCIF format, chain J [auth G] mmCIF format, chain K [auth G] mmCIF format, chain L [auth G] mmCIF format, chain M [auth G] mmCIF format, chain N [auth G] mmCIF format, chain O [auth G] mmCIF format, chain P [auth G] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A] BA [auth A] CA [auth A] G H [auth G] AA [auth A], BA [auth A], CA [auth A], G, H [auth G], I [auth G], J [auth G], K [auth G], L [auth G], M [auth G], N [auth G], O [auth G], P [auth G], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] 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] Focus chain N [auth G] Focus chain O [auth G] Focus chain P [auth G] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] 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] Focus chain N [auth G] Focus chain O [auth G] Focus chain P [auth G] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain Q [auth G] MOL2 format, chain DA [auth A] MOL2 format, chain Q [auth G] mmCIF format, chain DA [auth A] mmCIF format, chain Q [auth G]	DA [auth A], Q [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth A] Focus chain Q [auth G] Interactions & Density Focus chain DA [auth A] Focus chain Q [auth G]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain R [auth G] SDF format, chain S [auth G] MOL2 format, chain EA [auth A] MOL2 format, chain R [auth G] MOL2 format, chain S [auth G] mmCIF format, chain EA [auth A] mmCIF format, chain R [auth G] mmCIF format, chain S [auth G]	EA [auth A], R [auth G], S [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain R [auth G] Focus chain S [auth G] Interactions & Density Focus chain EA [auth A] Focus chain R [auth G] Focus chain S [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.292 (Depositor), 0.292 (DCC)
R-Value Work: 0.240 (Depositor), 0.239 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.209	α = 90.26
b = 68.211	β = 102.35
c = 115.055	γ = 90.38

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-30

Deposition Author(s):

Tolbert, W.D.

Pazgier, M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI116274
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI120756
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI129769

Revision History (Full details and data files)

Version 1.0: 2022-11-30
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary
Version 2.0: 2025-01-22
Type: Coordinate replacement
Reason: Polymer geometry
Changes: Atomic model, Data collection, Derived calculations, Other, Refinement description, Structure summary