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5lsd

Recombinant mouse Nerve Growth Factor

Method: SOLUTION NMR Dmax: 67.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Beta-nerve growth factor

Mus musculus

UniProt P01139

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 122–239 Chain B； UniProt 122–239 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；303 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR measurement conditions：pH 7；308 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition：0.1 mM [U-99% 13C; U-99% 15N] Nerve Growth Factor, 50 mM sodium phosphate, 1 mM EDTA, 93% H2O/7% D2O | 93% H2O/7% D2O Resolution not provided

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 5LSD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BET NEW PROTEIN FOLD REVEALED BY A 2.3 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF NERVE GROWTH FACTOR Deposited 1993-04-08 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 131–237（107 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1BTG CRYSTAL STRUCTURE OF BETA NERVE GROWTH FACTOR AT 2.5 A RESOLUTION IN C2 SPACE GROUP WITH ZN IONS BOUND Deposited 1995-08-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 130–239（110 aa）
Chain B 130–239（110 aa）
Chain C 130–239（110 aa）
Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED) Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED) Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED) ZN ZINC ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1BTG CRYSTAL STRUCTURE OF BETA NERVE GROWTH FACTOR AT 2.5 A RESOLUTION IN C2 SPACE GROUP WITH ZN IONS BOUND Deposited 1995-08-29 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 130–239（110 aa）
Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED) No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1BTG CRYSTAL STRUCTURE OF BETA NERVE GROWTH FACTOR AT 2.5 A RESOLUTION IN C2 SPACE GROUP WITH ZN IONS BOUND Deposited 1995-08-29 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 130–239（110 aa）
Chain C 130–239（110 aa）
Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED) Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED) ZN ZINC ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1BTG CRYSTAL STRUCTURE OF BETA NERVE GROWTH FACTOR AT 2.5 A RESOLUTION IN C2 SPACE GROUP WITH ZN IONS BOUND Deposited 1995-08-29 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 130–239（110 aa）
Chain C 130–239（110 aa）
Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED) Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED) ZN ZINC ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1SGF CRYSTAL STRUCTURE OF 7S NGF: A COMPLEX OF NERVE GROWTH FACTOR WITH FOUR BINDING PROTEINS (SERINE PROTEINASES) Deposited 1997-08-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 122–239（118 aa）
Chain Y 122–239（118 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.9；PROTEIN WAS CRYSTALLIZED FROM 20MG/ML PROTEIN SOLUTION IN 50MM SODIUM PHOSPHATE (PH6.8) MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION (50MM SODIUM ACETATE PH4.5-5.1, 12-21% PEG 4000, 10 MICROMOLAR ZNSO4) (MCDONALD AND BLUNDELL, 1991, JMB, 219, 595-601)., pH 4.9
Resolution 3.15 Å R-free 0.282
3IJ2 Ligand-receptor structure Deposited 2009-08-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 129–351（223 aa） Fragment：UNP RESIDUES 129-241
Chain B 129–351（223 aa） Fragment：UNP RESIDUES 129-241
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.75 Å R-free 0.274
4EAX Mouse NGF in complex with Lyso-PS Deposited 2012-03-23 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 122–241（120 aa）
Chain B 122–241（120 aa）
Not recorded S12 O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1M Imidazole, 1.0M Sodium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.30 Å R-free 0.259
4EAX Mouse NGF in complex with Lyso-PS Deposited 2012-03-23 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 122–241（120 aa）
Chain D 122–241（120 aa）
Not recorded S12 O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1M Imidazole, 1.0M Sodium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.30 Å R-free 0.259
4XPJ Crystal structure of Nerve growth factor in complex with lysophosphatidylinositol Deposited 2015-01-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 122–241（120 aa）
Chain B 122–241（120 aa）
Not recorded LPY (2R)-2-hydroxy-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl tridecanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1 M imidazole, 1.0 M Na acetate
Resolution 2.60 Å R-free 0.266
6FFY Structure of the mouse SorCS2-NGF complex Deposited 2018-01-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 122–238（117 aa）
Chain C 122–238（117 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；291 K；0.225 M MES/bis-tris pH 6.6 and 6.6 % w/v PEG 6000
Resolution 3.90 Å R-free 0.305

7 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NGF_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–118； UniProt 122–239 Author chain B； PDBConstruct 1–118； UniProt 122–239

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

SAXS profile for 5lsd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5lsd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5lsd
Deposition date deposition_date2016-08-25
Structure title titleRecombinant mouse Nerve Growth Factor
Keywords keywordsNGF, homodimer, cystin-knot, dimerfit_1, cell cycle; CELL CYCLE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.27 Å
Radius of gyration Rg (electron density) rg_electron19.97 Å
Forward intensity I(0) i04157770000.00
Molecular weight molecular_weight530440.0 kDa
Excluded volume excluded_volume656320 ų
Envelope volume envelope_volume75129 ų
Hydration-shell volume shell_volume26937 ų
Envelope diameter envelope_diameter74.2 Å
Shell Rg shell_rg30.52 Å
Envelope Rg envelope_rg23.25 Å
Shape Rg shape_rg19.95 Å
Total Rg total_rg20.17 Å
Total atoms total_atoms73440
Residues n_residues4720
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax67.1 Å
Rg (real space) rg_real20.27 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real4.1580e+09
I(0) uncertainty (real space) i0_real_error5.3870e+07
Rg (reciprocal space) rg_reciprocal20.27 Å
I(0) (reciprocal space) i0_reciprocal4158000000.0000
Solution quality estimate total_estimate0.8895
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.0 Å
Skewness Skewness skewness0.330
Kurtosis Kurtosis kurtosis-0.452
Angular range angular_range— – 0.3900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1605000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.996
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5lsda_
Class classg — Small proteins
Fold Fold foldg.17 — Cystine-knot cytokines
Superfamily Superfamily superfamilyg.17.1 — Cystine-knot cytokines
Family Family familyg.17.1.3 — Neurotrophin
Domain ID domain_idd5lsdb_
Class classg — Small proteins
Fold Fold foldg.17 — Cystine-knot cytokines
Superfamily Superfamily superfamilyg.17.1 — Cystine-knot cytokines
Family Family familyg.17.1.3 — Neurotrophin

CATH v4.4 (2 domains)

Domain ID domain_id5lsdA00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily10 — Cystine-knot cytokines
Domain ID domain_id5lsdB00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily10 — Cystine-knot cytokines
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8. Citations (1)

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9. Files and Curves (10)