SAXSdb — 4dkv

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1. Protein Identity and Related Structures Protein Identity & Related Structures

HIV-1 gp120 core

Human immunodeficiency virus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2-acetamido-2-deoxy-beta-D-glucopyranose × 11 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 N-(4-chlorophenyl)-N'-{(S)-[5-(2-hydroxyethyl)-4-methyl-1,3-thiazol-2-yl][(2S)-piperidin-2-yl]methyl}ethanediamide × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	2-acetamido-2-deoxy-beta-D-glucopyranose × 9 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 N-(4-chlorophenyl)-N'-{(S)-[5-(2-hydroxyethyl)-4-methyl-1,3-thiazol-2-yl][(2S)-piperidin-2-yl]methyl}ethanediamide × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q0ED31_9HIV1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–80； UniProt 43–122 Author chain A； PDBConstruct 83–185； UniProt 201–303 Author chain A； PDBConstruct 192–353； UniProt 325–486 Author chain B； PDBConstruct 1–80； UniProt 43–122 Author chain B； PDBConstruct 83–185； UniProt 201–303 Author chain B； PDBConstruct 192–353； UniProt 325–486

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4dkv
Deposition date deposition_date	2012-02-04
Structure title title	Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-10007
Keywords keywords	HIV-1 gp120, clade A/E, CD4 mimic, NBD-10007, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4dkv__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4dkv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4dkv__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	21.87 Å
Rg (electron density)	20.77 Å
Total Rg	21.75 Å
Atom count	2877
Residues	339
Excluded volume	50559 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4dkv__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4dkv__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	HIV-1 gp120 core
Molecular weight formula_weight	39160.4 kDa
Mutation mutation	V1V2 and V3 deletion, His 375 to Ser
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5922

VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	20

Entity 3 Entity 3 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	N-(4-chlorophenyl)-N'-{(S)-[5-(2-hydroxyethyl)-4-methyl-1,3-thiazol-2-yl][(2S)-piperidin-2-yl]methyl}ethanediamide
Molecular weight formula_weight	437.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	196

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4dkvA01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	40 — HIV Envelope Protein Gp120; Chain G
Homologous superfamily homologous superfamily	20 — Human immunodeficiency virus 1, Gp160, envelope glycoprotein

Domain ID domain_id	4dkvB01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	40 — HIV Envelope Protein Gp120; Chain G
Homologous superfamily homologous superfamily	20 — Human immunodeficiency virus 1, Gp160, envelope glycoprotein

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Unit-cell length a length_a	64.333 Å
Unit-cell length b length_b	68.773 Å
Unit-cell length c length_c	93.848 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.74 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.185 Å
Low-resolution limit resolution_low	27.602 Å
R factor r_factor	0.2017
R_work r_work	0.1999
R_free r_free	0.2349

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-10007

1. Protein Identity and Related Structures Protein Identity & Related Structures

HIV-1 gp120 core

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4dkv__assembly_1__model_1

4dkv__assembly_1__model_1 | I(q)

4dkv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-10007

1. Protein Identity and Related Structures Protein Identity & Related Structures

HIV-1 gp120 core

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4dkv__assembly_1__model_1

4dkv__assembly_1__model_1 | I(q)

4dkv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)