2ays

A conserved non-metallic binding site in the C-terminal lobe of lactoferrin: Structure of the complex of C-terminal lobe of bovine lactoferrin with N-acetyl galactosamine at 1.86 A resolution

Method: X-RAY DIFFRACTION Dmax: 69.4 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 2 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 361–708 Fragment:Lactoferrin lobe 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)-alpha-D-mannopyranose-(1-4)-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 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 ZN ZINC ION × 2 FE FE (III) ION × 1 CO3 CARBONATE ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.1M MES, 25% POLYETHYLENE GLYCOL MONOMETHYL ETHER 550, 0.01M ZINC SULPHATE , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.86 Å R-free 0.209

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 1–348; UniProt 361–708

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 2ays

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ays
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id2ays
Deposition date deposition_date2005-09-08
Structure title titleA conserved non-metallic binding site in the C-terminal lobe of lactoferrin: Structure of the complex of C-terminal lobe of bovine lactoferrin with N-acetyl galactosamine at 1.86 A resolution
Keywords keywordsC-lobe, complex, lactoferrin, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.70
Radius of gyration Rg (electron density) rg_electron19.62
Forward intensity I(0) i029121700.00
Molecular weight molecular_weight39447.0 kDa
Excluded volume excluded_volume48517 ų
Envelope volume envelope_volume57095 ų
Hydration-shell volume shell_volume23552 ų
Envelope diameter envelope_diameter69.7
Shell Rg shell_rg26.78
Envelope Rg envelope_rg19.82
Shape Rg shape_rg19.59
Total Rg total_rg20.60
Total atoms total_atoms2745
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 dmax69.4
Rg (real space) rg_real20.56
Rg uncertainty (real space) rg_real_error0.33
I(0) (real space) i0_real2.9120e+07
I(0) uncertainty (real space) i0_real_error3.2840e+05
Rg (reciprocal space) rg_reciprocal20.59
I(0) (reciprocal space) i0_reciprocal29120000.0000
Solution quality estimate total_estimate0.8715
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.1
Skewness Skewness skewness0.145
Kurtosis Kurtosis kurtosis-0.416
Angular range angular_range— – 0.3850 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha6649000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 1.000

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_idd2aysa_
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 (2 domains)

Domain ID domain_id2aysA01
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_id2aysA02
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)