5I9Q

Crystal structure of 3BNC55 Fab in complex with 426c.TM4deltaV1-3 gp120

PDB DOI: https://doi.org/10.2210/pdb5I9Q/pdb

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

Deposited: 2016-02-20 Released: 2016-05-04
Deposition Author(s): Scharf, L., Chen, C., Bjorkman, P.J.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation, American Cancer Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.270
R-Value Work: 0.251
R-Value Observed: 0.252

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: 178.72 kDa
Atom Count: 11,445
Modelled Residue Count: 1,506
Deposited Residue Count: 1,570
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
426c.TM4dV1-3 p120	A, B [auth G]	353	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for A0A0K1H6P9 (Human immunodeficiency virus 1) Explore A0A0K1H6P9 Go to UniProtKB: A0A0K1H6P9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0K1H6P9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3BNC55 Fab heavy chain	C [auth B], E [auth H]	225	Homo sapiens	Mutation(s): 0
Entity Groups
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
3BNC55 light chain	D [auth C], F [auth L]	207	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-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth D]	6		N-Glycosylation	Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	H [auth E]	4		N-Glycosylation	Interactions Focus chain H [auth E] Interactions & Density Focus chain H [auth E]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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 I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth G] SDF format, chain Q [auth G] SDF format, chain R [auth G] SDF format, chain U [auth C] SDF format, chain V [auth L] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth G] MOL2 format, chain U [auth C] MOL2 format, chain V [auth L]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], P [auth G], Q [auth G], R [auth G], U [auth C], V [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth G] Focus chain U [auth C] Focus chain V [auth L] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth G] Focus chain U [auth C] Focus chain V [auth L]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain S [auth G] MOL2 format, chain S [auth G]	S [auth G]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain S [auth G] Interactions & Density Focus chain S [auth G]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain T [auth G] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain T [auth G]	N [auth A], O [auth A], T [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth G] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.270
R-Value Work: 0.251
R-Value Observed: 0.252
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.85	α = 90
b = 122.85	β = 90
c = 264.96	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-05-04

Deposition Author(s):

Scharf, L.

Chen, C.

Bjorkman, P.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI100148
Bill & Melinda Gates Foundation	United States	1040753
American Cancer Society	United States	PF-13-076-01-MPC

Revision History (Full details and data files)

Version 1.0: 2016-05-04
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2019-12-11
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary