RCSB Protein Data Bank - RCSB PDB - 1YYL Structure Summary

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crystal structure of CD4M33, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b

DOI:10.2210/pdb1yyl/pdb

1YYL

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Primary Citation

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Molecular Description

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Classification:	Viral Protein/immune System
Structure Weight:	174812.02

Molecule:

Exterior membrane glycoprotein(GP120)

Polymer:

Type:

protein

Length:

313

Chains:

G, P

Fragment:

core

Mutation:

deletion mutant

Organism

Human immunodeficiency virus 1

Gene Name

env

UniProtKB:

| | P35961

Molecule:

antibody 17b light chain

Polymer:

Type:

protein

Length:

214

Chains:

L, Q

Fragment:

ANTIGEN-BINDING FRAGMENT, FAB

Organism

Homo sapiens

Molecule:

antibody 17b heavy chain

Polymer:

Type:

protein

Length:

229

Chains:

H, R

Fragment:

ANTIGEN-BINDING FRAGMENT, FAB

Organism

Homo sapiens

Molecule:

CD4M33, scorpion-toxin mimic of CD4

Polymer:

Type:

protein

Length:

Chains:

M, S

Source

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Polymer: 1

Scientific Name:

Human immunodeficiency virus 1

Taxonomy

Expression System:

Drosophila melanogaster

Polymer: 2

Scientific Name:

Homo sapiens

Taxonomy

Common Name:

Human

Expression System:

Mus musculus

Polymer: 3

Scientific Name:

Homo sapiens

Taxonomy

Common Name:

Human

Expression System:

Mus musculus

Polymer: 4

Scientific Name:

Synthetic construct

Taxonomy

Related PDB Entries

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Identifier	Details
1YYM	F23 complexed with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b

Ligand Chemical Component

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Identifier	Formula	Name	Interactions
NAG Search Download	C₈ H₁₅ N O₆	N-ACETYL-D-GLUCOSAMINE		Ligand Explorer
NDG Search Download	C₈ H₁₅ N O₆	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE		Ligand Explorer

Modified Residues

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Identifier	Formula	Parent	Type
MPT Search	C₃ H₆ O₂ S		nonPolymer
BIF Search	C₁₅ H₁₅ N O₂	PHE	lPeptideLinking
VLM Search	C₅ H₁₂ N₂ O		lPeptideLinking

External Domain Annotations Hide
SCOP Classification v1.75: 12 Domains - data from SCOP

CATH Classification v3.4.0: 10 Domains - data from CATH

Pfam Classification: 15 Domains - data from Pfam
Structural Biology Knowledgebase Data Hide

Data in orange boxes are gathered from external resources (when available).

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Biological Assembly 1

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Biological assembly 1 assigned by authors

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Deposition Summary

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Authors: Huang, C.C., Stricher, F., Martin, L., Decker, J.M., Majeed, S., Barthe, P., Hendrickson, W.A., Robinson, J., Roumestand, C., Sodroski, J., Wyatt, R., Shaw, G.M., Vita, C., Kwong, P.D.

Deposition:	2005-02-25
Release:	2005-05-03
Last Modified (REVDAT):	2011-07-13

Revision History Hide

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2011-07-13
Version format compliance

2011-07-13
Non-polymer description

Experimental Details

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Method: X-RAY DIFFRACTION
Exp. Data:
Structure Factors
EDS

Unit Cell:
	Length [Å]	Angles [°]
	a = 51.52	α = 90.00
	b = 157.84	β = 93.55
	c = 109.92	γ = 90.00

Molecule of the Month Hide
Epidermal Growth Factor

Nanobodies

Antibodies

Hemagglutinin