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1lpp

ANALOGS OF REACTION INTERMEDIATES IDENTIFY A UNIQUE SUBSTRATE BINDING SITE IN CANDIDA RUGOSA LIPASE

Method: X-RAY DIFFRACTION Dmax: 70.5 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

LIPASE

Candida rugosa

UniProt P20261

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 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–549 Not recorded 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 CA CALCIUM ION × 2 HDS 1-HEXADECANOSULFONIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.18 Å
2 Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–549 Not recorded 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 4 HDS 1-HEXADECANOSULFONIC ACID × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.18 Å

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.

Other PDB Difference from Current Entry 1LPP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CRL INSIGHTS INTO INTERFACIAL ACTIVATION FROM AN 'OPEN' STRUCTURE OF CANDIDA RUGOSA LIPASE Deposited 1993-03-02 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 16–549（534 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.06 Å
1LPM A STRUCTURAL BASIS FOR THE CHIRAL PREFERENCES OF LIPASES Deposited 1995-01-06 Different ligand/ion Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–549（549 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 2 MPA (1R)-MENTHYL HEXYL PHOSPHONATE GROUP × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.18 Å
1LPN ANALOGS OF REACTION INTERMEDIATES IDENTIFY A UNIQUE SUBSTRATE BINDING SITE IN CANDIDA RUGOSA LIPASE Deposited 1995-01-11 Different ligand/ion Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–549（549 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 2 DSC DODECANESULFONATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.18 Å
1LPN ANALOGS OF REACTION INTERMEDIATES IDENTIFY A UNIQUE SUBSTRATE BINDING SITE IN CANDIDA RUGOSA LIPASE Deposited 1995-01-11 Different ligand/ion Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–549（549 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 4 DSC DODECANESULFONATE ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.18 Å
1LPO ANALOGS OF REACTION INTERMEDIATES IDENTIFY A UNIQUE SUBSTRATE BINDING SITE IN CANDIDA RUGOSA LIPASE Deposited 1995-01-13 Different ligand/ion Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–549（549 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 2 HDS 1-HEXADECANOSULFONIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.18 Å
1LPS A STRUCTURAL BASIS FOR THE CHIRAL PREFERENCES OF LIPASES Deposited 1995-01-05 Different ligand/ion Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–549（549 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 2 MPC (1S)-MENTHYL HEXYL PHOSPHONATE GROUP × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.18 Å
1TRH TWO CONFORMATIONAL STATES OF CANDIDA RUGOSA LIPASE Deposited 1993-11-18 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 16–549（534 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
3RAR X-ray structure of a bound phosphonate transition state analog and enantioselectivity of Candida rugosa lipase toward chiral carboxylic acids Deposited 2011-03-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 16–549（534 aa） Fragment：unp residues 16-549
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 2 IAN methyl hydrogen (R)-[(R)-methoxy(phenyl)methyl]phosphonate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；296 K；40% (v/v) 2-methyl-2,4-pentanediol, 30 mM sodium acetate buffer and 30 mM CaCl2., pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.19 Å R-free 0.211
3RAR X-ray structure of a bound phosphonate transition state analog and enantioselectivity of Candida rugosa lipase toward chiral carboxylic acids Deposited 2011-03-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 16–549（534 aa） Fragment：unp residues 16-549
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 4 IAN methyl hydrogen (R)-[(R)-methoxy(phenyl)methyl]phosphonate × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；296 K；40% (v/v) 2-methyl-2,4-pentanediol, 30 mM sodium acetate buffer and 30 mM CaCl2., pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.19 Å R-free 0.211

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LIP1_CANRU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–549； UniProt 1–549

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 1lpp

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1lpp
Deposition date deposition_date1995-01-17
Structure title titleANALOGS OF REACTION INTERMEDIATES IDENTIFY A UNIQUE SUBSTRATE BINDING SITE IN CANDIDA RUGOSA LIPASE
Keywords keywordsHYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.30 Å
Radius of gyration Rg (electron density) rg_electron22.15 Å
Forward intensity I(0) i054678700.00
Molecular weight molecular_weight58351.0 kDa
Excluded volume excluded_volume73185 ų
Envelope volume envelope_volume81857 ų
Hydration-shell volume shell_volume29560 ų
Envelope diameter envelope_diameter71.8 Å
Shell Rg shell_rg30.15 Å
Envelope Rg envelope_rg22.29 Å
Shape Rg shape_rg22.12 Å
Total Rg total_rg23.11 Å
Total atoms total_atoms4104
Residues n_residues534
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax70.5 Å
Rg (real space) rg_real23.14 Å
Rg uncertainty (real space) rg_real_error0.27 Å
I(0) (real space) i0_real5.4680e+07
I(0) uncertainty (real space) i0_real_error6.4310e+05
Rg (reciprocal space) rg_reciprocal23.18 Å
I(0) (reciprocal space) i0_reciprocal54680000.0000
Solution quality estimate total_estimate0.9053
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.3 Å
Skewness Skewness skewness0.126
Kurtosis Kurtosis kurtosis-0.468
Angular range angular_range— – 0.3400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10620000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.982
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1lppa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.17 — Fungal lipases

CATH v4.4 (1 domains)

Domain ID domain_id1lppA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
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8. Citations (4)

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9. Files and Curves (10)