4zzm

Human ERK2 in complex with an irreversible inhibitor

Method: X-RAY DIFFRACTION Dmax: 71.4 Å Quality: REASONABLE

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

MITOGEN-ACTIVATED PROTEIN KINASE 1

HOMO SAPIENS

UniProt P28482

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 11–360 Fragment:KINASE DOMAIN, RESIDUES 11-360 Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 CQ6 7-ethylsulfonyl-N-(oxan-4-yl)-6,8-dihydro-5H-pyrido[3,4-d]pyrimidin-2-amine × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.89 Å R-free 0.254

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.

158 other PDB entries and 177 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MK01_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–350; UniProt 11–360

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 4zzm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4zzm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4zzm
Deposition date deposition_date2015-04-10
Structure title titleHuman ERK2 in complex with an irreversible inhibitor
Keywords keywordsTRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.16
Radius of gyration Rg (electron density) rg_electron21.11
Forward intensity I(0) i025087900.00
Molecular weight molecular_weight38955.0 kDa
Excluded volume excluded_volume49042 ų
Envelope volume envelope_volume57605 ų
Hydration-shell volume shell_volume22880 ų
Envelope diameter envelope_diameter72.7
Shell Rg shell_rg27.90
Envelope Rg envelope_rg21.27
Shape Rg shape_rg21.12
Total Rg total_rg21.98
Total atoms total_atoms2744
Residues n_residues344
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 dmax71.4
Rg (real space) rg_real22.08
Rg uncertainty (real space) rg_real_error0.38
I(0) (real space) i0_real2.5090e+07
I(0) uncertainty (real space) i0_real_error2.9600e+05
Rg (reciprocal space) rg_reciprocal22.10
I(0) (reciprocal space) i0_reciprocal25090000.0000
Solution quality estimate total_estimate0.6969
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.6
Skewness Skewness skewness0.291
Kurtosis Kurtosis kurtosis-0.312
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5352000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.999; Smooth: 0.978

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4zzma_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (2 domains)

Domain ID domain_id4zzmA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id4zzmA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1

8. Citations (1)

9. Files and Curves (10)