6ugs

Crystal structure of the Fab fragment of PF06438179/GP1111 an infliximab biosimilar in a C-centered orthorhombic crystal form, Lot A

Method: X-RAY DIFFRACTION Dmax: 108.2 Å Quality: GOOD

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

Infliximab (Remicade) Fab Heavy Chain

Homo sapiens

UniProt A8K008

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 H; UniProt 139–248 Not recorded Infliximab (Remicade) Fab Light Chain × 1 (Q6P5S8) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;289 K;10 mg/mL PF06438179 Fab lot A against 19.5% PEG 10000, 0.1 M HEPES pH 7.8, supplemented with 20% ethylene glycol as cryoprotectant, crystal tracking ID 267659h4, unique puck ID lqb9-8 Resolution 1.95 Å R-free 0.198
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 139–248 Not recorded Infliximab (Remicade) Fab Light Chain × 1 (Q6P5S8) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;289 K;10 mg/mL PF06438179 Fab lot A against 19.5% PEG 10000, 0.1 M HEPES pH 7.8, supplemented with 20% ethylene glycol as cryoprotectant, crystal tracking ID 267659h4, unique puck ID lqb9-8 Resolution 1.95 Å R-free 0.198

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.

10 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A8K008_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 117–226; UniProt 139–248 Author chain H; PDBConstruct 117–226; UniProt 139–248

Infliximab (Remicade) Fab Light Chain

Homo sapiens

UniProt Q6P5S8

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 L; UniProt 129–236 Not recorded Infliximab (Remicade) Fab Heavy Chain × 1 (A8K008) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;289 K;10 mg/mL PF06438179 Fab lot A against 19.5% PEG 10000, 0.1 M HEPES pH 7.8, supplemented with 20% ethylene glycol as cryoprotectant, crystal tracking ID 267659h4, unique puck ID lqb9-8 Resolution 1.95 Å R-free 0.198
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 129–236 Not recorded Infliximab (Remicade) Fab Heavy Chain × 1 (A8K008) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;289 K;10 mg/mL PF06438179 Fab lot A against 19.5% PEG 10000, 0.1 M HEPES pH 7.8, supplemented with 20% ethylene glycol as cryoprotectant, crystal tracking ID 267659h4, unique puck ID lqb9-8 Resolution 1.95 Å R-free 0.198

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.

16 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q6P5S8_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 107–214; UniProt 129–236 Author chain L; PDBConstruct 107–214; UniProt 129–236

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 6ugs

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6ugs
Deposition date deposition_date2019-09-26
Structure title titleCrystal structure of the Fab fragment of PF06438179/GP1111 an infliximab biosimilar in a C-centered orthorhombic crystal form, Lot A
Keywords keywordsantibody, Fab, infliximab, biosimilar, TNFa, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.06
Radius of gyration Rg (electron density) rg_electron31.29
Forward intensity I(0) i0142623000.00
Molecular weight molecular_weight92351.0 kDa
Excluded volume excluded_volume114360 ų
Envelope volume envelope_volume148620 ų
Hydration-shell volume shell_volume40184 ų
Envelope diameter envelope_diameter110.6
Shell Rg shell_rg38.02
Envelope Rg envelope_rg30.54
Shape Rg shape_rg31.30
Total Rg total_rg31.85
Total atoms total_atoms6506
Residues n_residues864
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 dmax108.2
Rg (real space) rg_real32.00
Rg uncertainty (real space) rg_real_error0.96
I(0) (real space) i0_real1.4260e+08
I(0) uncertainty (real space) i0_real_error2.3420e+06
Rg (reciprocal space) rg_reciprocal32.03
I(0) (reciprocal space) i0_reciprocal142600000.0000
Solution quality estimate total_estimate0.8813
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.8
Skewness Skewness skewness0.296
Kurtosis Kurtosis kurtosis-0.274
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17390000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.920

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd6ugsa_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd6ugsb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6ugsb2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd6ugsh_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd6ugsl1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6ugsl2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (4 domains)

Domain ID domain_id6ugsA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6ugsB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6ugsH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6ugsL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)