2p1s

Crystal structure of the C-terminal lobe of bovine lactoferrin complexed with O-alpha-D-Glucopyranosyl-(1 3)-alpha-D-fructofuranosyl- (2 1)- alpha-D-glucopyranoside at 1.93 A resolution

Method: X-RAY DIFFRACTION Dmax: 66.2 Å Quality: GOOD

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

Lactotransferrin

OrganismNot specified

UniProt P24627

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Monomer Protein × 1 其他Polymer 3 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 361–704 Fragment:c-terminal lobe(residues 342-685) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-galactopyranose-(1-2)-alpha-D-fructofuranose-(1-3)-alpha-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FE FE (III) ION × 1 CO3 CARBONATE ION × 1 ZN ZINC ION × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.8;298 K;0.1M HEPES, 0.2M ZnSO4, 20% PEG monomethyl ether, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.93 Å R-free 0.217

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.

86 other PDB entries and 89 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRFL_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–344; UniProt 361–704

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 2p1s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2p1s
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2p1s
Deposition date deposition_date2007-03-06
Structure title titleCrystal structure of the C-terminal lobe of bovine lactoferrin complexed with O-alpha-D-Glucopyranosyl-(1 3)-alpha-D-fructofuranosyl- (2 1)- alpha-D-glucopyranoside at 1.93 A resolution
Keywords keywordsLactoferrin, Sugar, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.66
Radius of gyration Rg (electron density) rg_electron19.58
Forward intensity I(0) i029153400.00
Molecular weight molecular_weight39423.0 kDa
Excluded volume excluded_volume48480 ų
Envelope volume envelope_volume56718 ų
Hydration-shell volume shell_volume23458 ų
Envelope diameter envelope_diameter69.7
Shell Rg shell_rg26.73
Envelope Rg envelope_rg19.78
Shape Rg shape_rg19.54
Total Rg total_rg20.56
Total atoms total_atoms2743
Residues n_residues340
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax66.2
Rg (real space) rg_real20.52
Rg uncertainty (real space) rg_real_error0.33
I(0) (real space) i0_real2.9150e+07
I(0) uncertainty (real space) i0_real_error3.6290e+05
Rg (reciprocal space) rg_reciprocal20.55
I(0) (reciprocal space) i0_reciprocal29150000.0000
Solution quality estimate total_estimate0.8110
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.9
Skewness Skewness skewness0.148
Kurtosis Kurtosis kurtosis-0.408
Angular range angular_range— – 0.3850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6717000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2p1sa_
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.94.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id2p1sA01
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_id2p1sA02
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

8. Citations (1)

9. Files and Curves (10)