2aj3

Crystal Structure of a Cross-Reactive HIV-1 Neutralizing CD4-Binding Site Antibody Fab m18

Method: X-RAY DIFFRACTION D_max: 193.4 Å Quality: REASONABLE

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

Fab m18, Light Chain

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 25–236	Not recorded	Fab m18, Heavy Chain × 1 （Q6GMX1） SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；292 K；100 mM CHES, 20% (w/v) PEG-8000, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.03 Å R-free 0.269
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 25–236	Not recorded	Fab m18, Heavy Chain × 1 （Q6GMX1） SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；292 K；100 mM CHES, 20% (w/v) PEG-8000, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.03 Å R-free 0.269
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 25–236	Not recorded	Fab m18, Heavy Chain × 1 （Q6GMX1） SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；292 K；100 mM CHES, 20% (w/v) PEG-8000, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.03 Å R-free 0.269

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2AJ3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2HFG Crystal structure of hBR3 bound to CB3s-Fab Deposited 2006-06-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 23–236（214 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions Drops contained 2.1 microliters protein solution (pH 6.5) and 2.9 microliters of (0.1M citric acid pH 3.0, 24% PEG 3350, and 0.1 M Praseodymium (III) acetate) over a reservoir of 24% PEG 3350. pH of final drop ~4.5.	Resolution 2.61 Å R-free 0.252

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6PIH7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–213； UniProt 25–236 Author chain C； PDBConstruct 2–213； UniProt 25–236 Author chain E； PDBConstruct 2–213； UniProt 25–236

Fab m18, Heavy Chain

Homo sapiens

UniProt Q6GMX1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 21–252	Not recorded	Fab m18, Light Chain × 1 （Q6PIH7） SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；292 K；100 mM CHES, 20% (w/v) PEG-8000, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.03 Å R-free 0.269
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 21–252	Not recorded	Fab m18, Light Chain × 1 （Q6PIH7） SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；292 K；100 mM CHES, 20% (w/v) PEG-8000, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.03 Å R-free 0.269
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 21–252	Not recorded	Fab m18, Light Chain × 1 （Q6PIH7） SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；292 K；100 mM CHES, 20% (w/v) PEG-8000, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.03 Å R-free 0.269

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q6GMX1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–227； UniProt 21–252 Author chain D； PDBConstruct 1–227； UniProt 21–252 Author chain F； PDBConstruct 1–227； UniProt 21–252

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2aj3
Deposition date deposition_date	2005-08-01
Structure title title	Crystal Structure of a Cross-Reactive HIV-1 Neutralizing CD4-Binding Site Antibody Fab m18
Keywords keywords	HIV, antibody, Fab, CD4-binding, immunoglobulin, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	57.79 Å
Radius of gyration Rg (electron density) rg_electron	59.49 Å
Forward intensity I(0) i0	301657000.00
Molecular weight molecular_weight	141970.0 kDa
Excluded volume excluded_volume	176870 Å³
Envelope volume envelope_volume	260230 Å³
Hydration-shell volume shell_volume	43918 Å³
Envelope diameter envelope_diameter	205.5 Å
Shell Rg shell_rg	46.10 Å
Envelope Rg envelope_rg	59.42 Å
Shape Rg shape_rg	59.48 Å
Total Rg total_rg	59.07 Å
Total atoms total_atoms	9998
Residues n_residues	1280
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	193.4 Å
Rg (real space) rg_real	59.07 Å
Rg uncertainty (real space) rg_real_error	2.08 Å
I(0) (real space) i0_real	3.0160e+08
I(0) uncertainty (real space) i0_real_error	6.5870e+06
Rg (reciprocal space) rg_reciprocal	56.68 Å
I(0) (reciprocal space) i0_reciprocal	300500000.0000
Solution quality estimate total_estimate	0.6606
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.8 Å
Skewness Skewness skewness	0.642
Kurtosis Kurtosis kurtosis	-0.445
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	9902000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.418; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.170; Smooth: 0.159

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Fab m18, Light Chain
Molecular weight formula_weight	23441.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	10497

LQMTQSPSFLSASVGDRVSITCRASQDIQKFLAWYQLTPGDAPKLLMYSASTLQSGVPSRFSGSGSGTEFTLTISGLQPEDFATYYCQHLKRYPYTFGQGTKLEISRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDNKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Fab m18, Heavy Chain
Molecular weight formula_weight	24423.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F

VQLLESGPGVVKPSETLSLTCTVSGASVNNYYWTWVRQPPGKGLEWIGNVYDSGDTNYNPSLSSRLSLSMDTSKNQFSLRLSSVTAADTATYYCARYHRHFIRGPLSFDYWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTSALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	499

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7. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2aj3a1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d2aj3a2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2aj3b_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d2aj3c1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d2aj3c2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2aj3d_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d2aj3e1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d2aj3e2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2aj3f_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	2aj3A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2aj3A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2aj3B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2aj3B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2aj3C01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2aj3C02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2aj3D01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2aj3D02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2aj3E01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2aj3E02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2aj3F01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2aj3F02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	48.599 Å
Unit-cell length b length_b	82.620 Å
Unit-cell length c length_c	187.204 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.27 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.030 Å
Low-resolution limit resolution_low	29.250 Å
R factor r_factor	0.2270
R_work r_work	0.2250
R_free r_free	0.2690

fit	/app/data/saxs_computation/aj/2aj3/2aj3.fit
pddf	/app/data/pr_computation/aj/2aj3/2aj3.pr.out
profile	/app/data/saxs_computation/aj/2aj3/2aj3.dat

Crystal Structure of a Cross-Reactive HIV-1 Neutralizing CD4-Binding Site Antibody Fab m18

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

Fab m18, Light Chain

State in the Current Structure

Other States of the Same Protein in the Database

Fab m18, Heavy Chain

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (9 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)