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1lfh

MOLECULAR REPLACEMENT SOLUTION OF THE STRUCTURE OF APOLACTOFERRIN, A PROTEIN DISPLAYING LARGE-SCALE CONFORMATIONAL CHANGE

Method: X-RAY DIFFRACTION Dmax: 95.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

LACTOFERRIN

Homo sapiens

UniProt P02788

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 22–711 Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å

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 1LFH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B0L RECOMBINANT HUMAN DIFERRIC LACTOFERRIN Deposited 1998-11-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–710（691 aa）
Mutation：A10T FE FE (III) ION × 2 CO3 CARBONATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；DIALYSIS AGAINST 10MM SODIUM PHOSPHATE PH 8.0, CONTAINING 10% ETHANOL
Resolution 2.20 Å R-free 0.274
1BKA OXALATE-SUBSTITUTED DIFERRIC LACTOFERRIN Deposited 1996-04-15 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–711（692 aa）
Not recorded FE FE (III) ION × 2 OXL OXALATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
1CB6 STRUCTURE OF HUMAN APOLACTOFERRIN AT 2.0 A RESOLUTION. Deposited 1999-03-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–710（691 aa） Fragment：UNP residues 20-710
Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；pH 7.8
Resolution 2.00 Å R-free 0.286
1DSN D60S N-TERMINAL LOBE HUMAN LACTOFERRIN Deposited 1995-12-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–353（333 aa） Fragment：N-TERMINAL LOBE RESIDUES 1 - 333
Mutation：D60S FE FE (III) ION × 1 CO3 CARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 2.05 Å
1EH3 R210K N-TERMINAL LOBE HUMAN LACTOFERRIN Deposited 2000-02-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 15–348（334 aa） Fragment：N-TERMINAL LOBE
Mutation：R210K FE FE (III) ION × 1 CO3 CARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIQUID DIFFUSION；pH 8；277 K；HEPES, NaCl, pH 8.0, LIQUID DIFFUSION, temperature 4K
Resolution 2.00 Å R-free 0.250
1FCK STRUCTURE OF DICERIC HUMAN LACTOFERRIN Deposited 2000-07-18 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–711（692 aa）
Not recorded CO3 CARBONATE ION × 2 CE CERIUM (III) ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.257
1H43 R210E N-TERMINAL LOBE HUMAN LACTOFERRIN Deposited 2002-10-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–353（334 aa） Fragment：N-TERMINAL LOBE, RESIDUES 20-353
Mutation：YES CO3 CARBONATE ION × 1 FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；HEPES, NACL, pH 8.00
Resolution 2.20 Å R-free 0.235
1H44 R210L N-TERMINAL LOBE HUMAN LACTOFERRIN Deposited 2002-10-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–353（334 aa） Fragment：N-TERMINAL LOBE, RESIDUES 20-353
Mutation：YES FE FE (III) ION × 1 CO3 CARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；HEPES, NACL, pH 8.00
Resolution 2.00 Å R-free 0.241
1H45 R210G N-TERMINAL LOBE HUMAN LACTOFERRIN Deposited 2002-10-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–353（334 aa） Fragment：N-TERMINAL LOBE, RESIDUES 20-353
Mutation：YES FE FE (III) ION × 1 CO3 CARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；HEPES, NACL, pH 8.00
Resolution 1.95 Å R-free 0.248
1HSE H253M N TERMINAL LOBE OF HUMAN LACTOFERRIN Deposited 1996-12-11 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–347（327 aa） Fragment：N-TERMINAL HALF-MOLECULE
Mutation：H253M FE FE (III) ION × 1 CO3 CARBONATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
1L5T Crystal Structure of a Domain-Opened Mutant (R121D) of the Human Lactoferrin N-lobe Refined From a Merohedrally-Twinned Crystal Form. Deposited 2002-03-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–352（332 aa） Fragment：RESIDUES 21-352
Mutation：R121D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 8；298 K；concentrated solution of the protein (50-80 mg mL-1), 0.01 M Tris-HCl, pH 8.0, 12% (v/v) isopropanol, MICRODIALYSIS, temperature 298K
Resolution 3.00 Å R-free 0.199
1L5T Crystal Structure of a Domain-Opened Mutant (R121D) of the Human Lactoferrin N-lobe Refined From a Merohedrally-Twinned Crystal Form. Deposited 2002-03-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 21–352（332 aa） Fragment：RESIDUES 21-352
Mutation：R121D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 8；298 K；concentrated solution of the protein (50-80 mg mL-1), 0.01 M Tris-HCl, pH 8.0, 12% (v/v) isopropanol, MICRODIALYSIS, temperature 298K
Resolution 3.00 Å R-free 0.199
1LCF CRYSTAL STRUCTURE OF COPPER-AND OXALATE-SUBSTITUTED HUMAN LACTOFERRIN AT 2.0 ANGSTROMS RESOLUTION Deposited 1994-01-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–711（690 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CU COPPER (II) ION × 2 CO3 CARBONATE ION × 1 OXL OXALATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1LCT STRUCTURE OF THE RECOMBINANT N-TERMINAL LOBE OF HUMAN LACTOFERRIN AT 2.0 ANGSTROMS RESOLUTION Deposited 1993-06-19 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–353（333 aa）
Not recorded FE FE (III) ION × 1 CO3 CARBONATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1LFG Structure of diferric human lactoferrin Deposited 1992-02-05 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–711（690 aa）
Not recorded FE FE (III) ION × 2 CO3 CARBONATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
1LFI METAL SUBSTITUTION IN TRANSFERRINS: THE CRYSTAL STRUCTURE OF HUMAN COPPER-LACTOFERRIN AT 2.1 ANGSTROMS RESOLUTION Deposited 1992-02-10 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–711（690 aa）
Not recorded CU COPPER (II) ION × 2 CO3 CARBONATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
1LGB INTERACTION OF A LEGUME LECTIN WITH THE N2 FRAGMENT OF HUMAN LACTOTRANSFERRIN OR WITH THE ISOLATED BIANTENNARY GLYCOPEPTIDE: ROLE OF THE FUCOSE MOIETY Deposited 1994-01-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 111–269（159 aa）
Not recorded MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.30 Å
1LGB INTERACTION OF A LEGUME LECTIN WITH THE N2 FRAGMENT OF HUMAN LACTOTRANSFERRIN OR WITH THE ISOLATED BIANTENNARY GLYCOPEPTIDE: ROLE OF THE FUCOSE MOIETY Deposited 1994-01-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 111–269（159 aa）
Not recorded MN MANGANESE (II) ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.30 Å
1N76 CRYSTAL STRUCTURE OF HUMAN SEMINAL LACTOFERRIN AT 3.4 A RESOLUTION Deposited 2002-11-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–711（690 aa）
Not recorded NA SODIUM ION × 1 FE FE (III) ION × 2 CO3 CARBONATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 8；298 K；Tris-HCl, ethanol, pH 8.0, MICRODIALYSIS, temperature 298.0K
Resolution 3.40 Å R-free 0.266
1SQY Structure of human diferric lactoferrin at 2.5A resolution using crystals grown at pH 6.5 Deposited 2004-03-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–710（691 aa）
Not recorded FE FE (III) ION × 2 CO3 CARBONATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 6.5；277 K；Ethanol, Tris-HCL, pH 6.5, MICRODIALYSIS, temperature 277K
Resolution 2.50 Å R-free 0.215
1U62 NMR structure analysis of the lactoferrin-based peptide FQWQRNIRKVR in complex with lipopolysaccharide Deposited 2004-07-29 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 39–49（11 aa） Fragment：LF11
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；303 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition 2mM lacfotefficin; 20mM sodium phosphate buffer (pH=5.5); 95% H2O, 5% D2O | 95% H2O/5% D2O
Resolution not provided
1VFD HUMAN LACTOFERRIN, N-TERMINAL LOBE MUTANT WITH ARG 121 REPLACED BY GLU (R121E) Deposited 1996-10-01 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–350（329 aa） Fragment：N-TERMINAL HALF-MOLECULE
Mutation：R121E FE FE (III) ION × 1 CO3 CARBONATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.310
1VFE HUMAN LACTOFERRIN, N-TERMINAL LOBE MUTANT WITH ARG 121 REPLACED BY SER (R121S) Deposited 1996-10-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–353（332 aa） Fragment：N-TERMINAL HALF-MOLECULE
Mutation：R121S FE FE (III) ION × 1 CO3 CARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；50MM TRIS/HCL PH 8.0, 12% ISOPROPANOL
Resolution 2.30 Å R-free 0.270
1Z6V Human lactoferricin Deposited 2005-03-23 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–68（49 aa） Fragment：N-terminal peptide
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3；298 K；Ionic strength (raw mmCIF value) no salt added；Pressure ambient
NMR sample composition 1mM lactoferricin | 4:4:1 chloroform-d:methanol-d3:D2O
Resolution not provided
1Z6W Human Lactoferricin Deposited 2005-03-23 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–68（49 aa） Fragment：N-terminal peptide
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3.5；298 K；Ionic strength (raw mmCIF value) no salt added；Pressure ambient
NMR sample composition 1mM lactoferricin | 90% H20, 10% D2O
Resolution not provided
2BJJ Structure of recombinant human lactoferrin produced in the milk of transgenic cows Deposited 2005-02-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 20–711（692 aa）
Not recorded FE FE (III) ION × 2 CO3 CARBONATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；5 MM SODIUM PHOSPHATE PH 8.5, 10% (V/V) ETHANOL
Resolution 2.40 Å R-free 0.231
2DP4 Crystal structure of the complex formed between proteinase K and a human lactoferrin fragment at 2.9 A resolution Deposited 2006-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 528–535（8 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M Ammonium actate, 0.1M sodium acetate, 30% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.90 Å R-free 0.235
7N88 The cryoEM structure of LbpB from N. gonorrhoeae in complex with lactoferrin Deposited 2021-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 20–710（691 aa）
Not recorded FE FE (III) ION × 2 BCT BICARBONATE ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

26 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRFL_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–691； UniProt 22–711

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 1lfh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1lfh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1lfh
Deposition date deposition_date1991-09-04
Structure title titleMOLECULAR REPLACEMENT SOLUTION OF THE STRUCTURE OF APOLACTOFERRIN, A PROTEIN DISPLAYING LARGE-SCALE CONFORMATIONAL CHANGE
Keywords keywordsIRON TRANSPORT; IRON TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.47 Å
Radius of gyration Rg (electron density) rg_electron28.46 Å
Forward intensity I(0) i0100153000.00
Molecular weight molecular_weight76169.0 kDa
Excluded volume excluded_volume94279 ų
Envelope volume envelope_volume116260 ų
Hydration-shell volume shell_volume34203 ų
Envelope diameter envelope_diameter99.5 Å
Shell Rg shell_rg35.56 Å
Envelope Rg envelope_rg28.43 Å
Shape Rg shape_rg28.44 Å
Total Rg total_rg29.18 Å
Total atoms total_atoms5343
Residues n_residues691
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 dmax95.8 Å
Rg (real space) rg_real29.43 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real1.0020e+08
I(0) uncertainty (real space) i0_real_error1.5360e+06
Rg (reciprocal space) rg_reciprocal29.45 Å
I(0) (reciprocal space) i0_reciprocal100200000.0000
Solution quality estimate total_estimate0.9031
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary— Å
Skewness Skewness skewness0.253
Kurtosis Kurtosis kurtosis-0.539
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha20430000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.981
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1lfha1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.2 — Transferrin
Domain ID domain_idd1lfha2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.2 — Transferrin

CATH v4.4 (4 domains)

Domain ID domain_id1lfhA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id1lfhA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id1lfhA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id1lfhA04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
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8. Citations (5)

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9. Files and Curves (10)