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Open data
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Basic information
Entry | Database: PDB / ID: 1lfg | |||||||||
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Title | Structure of diferric human lactoferrin | |||||||||
![]() | LACTOFERRIN | |||||||||
![]() | TRANSFERRIN | |||||||||
Function / homology | ![]() negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / negative regulation of viral process / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism ...negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / negative regulation of viral process / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of lipopolysaccharide-mediated signaling pathway / specific granule / negative regulation of osteoclast development / antifungal humoral response / positive regulation of chondrocyte proliferation / negative regulation of ATP-dependent activity / regulation of tumor necrosis factor production / bone morphogenesis / Antimicrobial peptides / cysteine-type endopeptidase inhibitor activity / negative regulation of viral genome replication / positive regulation of osteoblast proliferation / humoral immune response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of osteoblast differentiation / regulation of cytokine production / protein serine/threonine kinase activator activity / ossification / innate immune response in mucosa / secretory granule / lipopolysaccharide binding / positive regulation of protein serine/threonine kinase activity / recycling endosome / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / positive regulation of NF-kappaB transcription factor activity / heparin binding / iron ion transport / antibacterial humoral response / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / killing of cells of another organism / early endosome / iron ion binding / Amyloid fiber formation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / protein-containing complex / proteolysis / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Baker, E.N. / Anderson, B.F. / Haridas, M. | |||||||||
![]() | ![]() Title: Structure of human diferric lactoferrin refined at 2.2 A resolution. Authors: Haridas, M. / Anderson, B.F. / Baker, E.N. #1: ![]() Title: Structure of Human Lactoferrin: Crystallographic Structure Analysis and Refinement at 2.8 Angstroms Resolution Authors: Anderson, B.F. / Baker, H.M. / Norris, G.E. / Rice, D.W. / Baker, E.N. #2: ![]() Title: Transferrins: Insights Into Structure and Function from Studies on Lactoferrin Authors: Baker, E.N. / Rumball, S.V. / Anderson, B.F. #3: ![]() Title: Structure of Human Lactoferrin at 3.2 Angstroms Resolution Authors: Anderson, B.F. / Baker, H.M. / Dodson, E.J. / Norris, G.E. / Rumball, S.V. / Waters, J.M. / Baker, E.N. | |||||||||
History |
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Remark 700 | SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS ...SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS *N2A* AND *N2B* REPRESENT ONE BIFURCATED SHEET WHERE STRAND 4 OF SHEET RECORD BN1 IS ALSO PART OF THIS SHEET. SHEETS *C2A* AND *C2B* REPRESENT ONE BIFURCATED SHEET WHERE STRAND 4 OF SHEET RECORD BC1 IS ALSO PART OF THIS SHEET. | |||||||||
Remark 650 | HELIX ON HELIX RECORDS THE TYPES OF DISTORTION IN H BONDING OF N AND C TERMINI CLASSIFIED AS IN F.N. ...HELIX ON HELIX RECORDS THE TYPES OF DISTORTION IN H BONDING OF N AND C TERMINI CLASSIFIED AS IN F.N.BAKER AND R.F.HUBBARD (1984) PROG. BIOPHYS. MOL. BIOL. 44, 97-179. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.1 KB | Display | ![]() |
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PDB format | ![]() | 124.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 518.5 KB | Display | ![]() |
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Full document | ![]() | 577.7 KB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 35.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 71 / 2: CIS PROLINE - PRO 142 / 3: CIS PROLINE - PRO 628 / 4: RESIDUES 1-4 POORLY DEFINED DENSITY. / 5: RESIDUES 293-294 POORLY DEFINED DENSITY. / 6: RESIDUES 418-422 POORLY DEFINED DENSITY. / 7: ASN 137 CARBOHYDRATE ATTACHMENT SITE. / 8: ASN 478 CARBOHYDRATE ATTACHMENT SITE. 9: NO SIDECHAINS BEYOND CB FOR ARG 86 AND GLU 637 (TREATED AS ALA). |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 76079.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 497 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | TWO-FOLD INTERNAL SEQUENCE HOMOLOGY (~ 40% IDENTITY). ONE BINDING SITE IN EACH LOBE. | ||
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Nonpolymer details | VERY POOR DENSITY FOR THE CARBOHYDRASequence details | AMINO ACID SEQUENCE GIVEN IN ANDERSON ET AL. (1989) (COMPOSITE OF CHEMICALLY-DETERMINED AND CDNA ...AMINO ACID SEQUENCE GIVEN IN ANDERSON ET AL. (1989) (COMPOSITE OF CHEMICALLY | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.94 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.8 / Method: microdialysisDetails: taken from Baker, E.N. et al (1977). J. Mol. Biol., 111, 207-210. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Num. obs: 17783 / Rmerge(I) obs: 0.09 |
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Processing
Software | Name: PROFFT / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.183 / Highest resolution: 2.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.2 Å
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Refine LS restraints |
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Software | *PLUS Name: PROFT / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.183 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 0.055 |