1xxm

The modular architecture of protein-protein binding site

Method: X-RAY DIFFRACTION Dmax: 170.6 Å Quality: REASONABLE

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

Beta-lactamase TEM

Escherichia coli

UniProt P62593

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 24–286 Mutation:E104A; Y105A Beta-lactamase inhibitory protein × 1 (P35804) CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 5;298 K;LiCl; sodium Acetate; PEG 6000, pH 5., Microbatch, temperature 298K Resolution 1.90 Å R-free 0.247
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 24–286 Mutation:E104A; Y105A Beta-lactamase inhibitory protein × 1 (P35804) CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 5;298 K;LiCl; sodium Acetate; PEG 6000, pH 5., Microbatch, temperature 298K Resolution 1.90 Å R-free 0.247

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.

72 other PDB entries and 154 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BLAT_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–263; UniProt 24–286 Author chain B; PDBConstruct 1–263; UniProt 24–286

Beta-lactamase inhibitory protein

Streptomyces clavuligerus

UniProt P35804

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 C; UniProt 37–201 Mutation:K74A; F142A; Y143A Beta-lactamase TEM × 1 (P62593) CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 5;298 K;LiCl; sodium Acetate; PEG 6000, pH 5., Microbatch, temperature 298K Resolution 1.90 Å R-free 0.247
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 37–201 Mutation:K74A; F142A; Y143A Beta-lactamase TEM × 1 (P62593) CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 5;298 K;LiCl; sodium Acetate; PEG 6000, pH 5., Microbatch, temperature 298K Resolution 1.90 Å R-free 0.247

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.

17 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BLIP_STRCL
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–165; UniProt 37–201 Author chain D; PDBConstruct 1–165; UniProt 37–201

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 1xxm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1xxm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1xxm
Deposition date deposition_date2004-11-07
Structure title titleThe modular architecture of protein-protein binding site
Keywords keywords;PROTEIN-PROTEIN COMPLEX; TEM-1 BETA-LACTAMASE; BETA-2 LACTAMASE INHIBITOR PROTEIN; BLIP, Israel Structural Proteomics Center, ISPC, Structural Genomics, HYDROLASE-HYDROLASE INHIBITOR COMPLEX ;; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier52.87
Radius of gyration Rg (electron density) rg_electron53.14
Forward intensity I(0) i0127028000.00
Molecular weight molecular_weight92205.0 kDa
Excluded volume excluded_volume114570 ų
Envelope volume envelope_volume177360 ų
Hydration-shell volume shell_volume27494 ų
Envelope diameter envelope_diameter153.5
Shell Rg shell_rg60.56
Envelope Rg envelope_rg49.14
Shape Rg shape_rg53.14
Total Rg total_rg53.37
Total atoms total_atoms6470
Residues n_residues856
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 dmax170.6
Rg (real space) rg_real53.28
Rg uncertainty (real space) rg_real_error2.77
I(0) (real space) i0_real1.2700e+08
I(0) uncertainty (real space) i0_real_error3.0450e+06
Rg (reciprocal space) rg_reciprocal52.46
I(0) (reciprocal space) i0_reciprocal126900000.0000
Solution quality estimate total_estimate0.5446
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary28.4
Skewness Skewness skewness0.123
Kurtosis Kurtosis kurtosis-1.508
Angular range angular_range— – 0.1500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4598000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.001; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.075; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1xxma_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamilye.3.1 — beta-lactamase/transpeptidase-like
Family Family familye.3.1.1 — beta-Lactamase/D-ala carboxypeptidase
Domain ID domain_idd1xxmb_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamilye.3.1 — beta-lactamase/transpeptidase-like
Family Family familye.3.1.1 — beta-Lactamase/D-ala carboxypeptidase
Domain ID domain_idd1xxmc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.98 — BLIP-like
Superfamily Superfamily superfamilyd.98.1 — beta-lactamase-inhibitor protein, BLIP
Family Family familyd.98.1.1 — beta-lactamase-inhibitor protein, BLIP
Domain ID domain_idd1xxmd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.98 — BLIP-like
Superfamily Superfamily superfamilyd.98.1 — beta-lactamase-inhibitor protein, BLIP
Family Family familyd.98.1.1 — beta-lactamase-inhibitor protein, BLIP

CATH v4.4 (6 domains)

Domain ID domain_id1xxmA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
Domain ID domain_id1xxmB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
Domain ID domain_id1xxmC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1450 — Beta-lactamase Inhibitory Protein; Chain:B, domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id1xxmC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1450 — Beta-lactamase Inhibitory Protein; Chain:B, domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id1xxmD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1450 — Beta-lactamase Inhibitory Protein; Chain:B, domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id1xxmD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1450 — Beta-lactamase Inhibitory Protein; Chain:B, domain 1
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)