6m5e

Human serum albumin with cyclic peptide dalbavancin

Method: X-RAY DIFFRACTION Dmax: 163.8 Å Quality: GOOD

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

Serum albumin

Homo sapiens

UniProt P02768

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 26–606 Not recorded dalbavancin × 1 JEF O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) × 2 F8F (2S,5S)-5-azanyl-3,4,6-tris(oxidanyl)oxane-2-carboxylic acid × 1 M12 10-METHYLUNDECANOIC ACID × 1 MAN alpha-D-mannopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277 K;0.1 M Sodium citrate tribasic dihydrate pH 5.0 30 % v/v Jeffamine ED-2001 pH 7.0 Resolution 2.80 Å R-free 0.228
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 26–606 Not recorded dalbavancin × 1 dalbavancin × 1 JEF O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) × 2 F8F (2S,5S)-5-azanyl-3,4,6-tris(oxidanyl)oxane-2-carboxylic acid × 1 M12 10-METHYLUNDECANOIC ACID × 2 MAN alpha-D-mannopyranose × 1 F8X 2-amino-2-deoxy-beta-D-altropyranuronic acid × 1 WOO beta-L-allopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277 K;0.1 M Sodium citrate tribasic dihydrate pH 5.0 30 % v/v Jeffamine ED-2001 pH 7.0 Resolution 2.80 Å R-free 0.228
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 26–606 Not recorded dalbavancin × 1 dalbavancin × 1 JEF O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) × 2 F8F (2S,5S)-5-azanyl-3,4,6-tris(oxidanyl)oxane-2-carboxylic acid × 1 M12 10-METHYLUNDECANOIC ACID × 2 MAN alpha-D-mannopyranose × 1 F8X 2-amino-2-deoxy-beta-D-altropyranuronic acid × 1 WOO beta-L-allopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277 K;0.1 M Sodium citrate tribasic dihydrate pH 5.0 30 % v/v Jeffamine ED-2001 pH 7.0 Resolution 2.80 Å R-free 0.228

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.

187 other PDB entries and 269 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ALBU_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–582; UniProt 26–606 Author chain B; PDBConstruct 2–582; UniProt 26–606 Author chain C; PDBConstruct 2–582; UniProt 26–606

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 6m5e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6m5e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6m5e
Deposition date deposition_date2020-03-10
Structure title titleHuman serum albumin with cyclic peptide dalbavancin
Keywords keywordsTransporter, Cyclic peptide, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier45.34
Radius of gyration Rg (electron density) rg_electron45.32
Forward intensity I(0) i0640969000.00
Molecular weight molecular_weight208370.0 kDa
Excluded volume excluded_volume260690 ų
Envelope volume envelope_volume370950 ų
Hydration-shell volume shell_volume70648 ų
Envelope diameter envelope_diameter173.6
Shell Rg shell_rg48.01
Envelope Rg envelope_rg44.32
Shape Rg shape_rg45.32
Total Rg total_rg45.44
Total atoms total_atoms14582
Residues n_residues1748
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 dmax163.8
Rg (real space) rg_real45.54
Rg uncertainty (real space) rg_real_error1.81
I(0) (real space) i0_real6.4100e+08
I(0) uncertainty (real space) i0_real_error1.1940e+07
Rg (reciprocal space) rg_reciprocal45.34
I(0) (reciprocal space) i0_reciprocal640800000.0000
Solution quality estimate total_estimate0.8404
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary51.5
Skewness Skewness skewness0.500
Kurtosis Kurtosis kurtosis-0.106
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha83850000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.705; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.910; Smooth: 0.897

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

7. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

Domain ID domain_id6m5eA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m5eA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m5eA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m5eA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m5eA05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m5eB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m5eB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m5eB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m5eB04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m5eB05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m5eC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m5eC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m5eC03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m5eC04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id6m5eC05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)