← Back to search
2gkj

Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor DL-AZIDAP

Method: X-RAY DIFFRACTION Dmax: 60.5 Å Quality: GOOD
▼

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

Diaminopimelate epimerase

Haemophilus influenzae

UniProt P44859

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 1–274 Not recorded ZDR (2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID × 1 ACY ACETIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.8 M sodium acetate and 0.1 M HEPES (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.70 Å R-free 0.210

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 2GKJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BWZ DIAMINOPIMELATE EPIMERASE FROM HEMOPHILUS INFLUENZAE Deposited 1998-09-29 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–274（274 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.72 Å R-free 0.242
1GQZ Refinement of Haemophilus influenzae Diaminopimelate epimerase at 1.7A Deposited 2001-12-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–274（274 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1M IMIDIZOLE PH 6.5,
Resolution 1.75 Å R-free 0.196
2GKE Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor LL-AziDAP Deposited 2006-04-01 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–274（274 aa）
Not recorded ZDP (2S,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID × 1 GOL GLYCEROL × 1 ACY ACETIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.8 M sodium acetate and 0.1 M HEPES (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.35 Å R-free 0.168
2Q9H Crystal structure of the C73S mutant of diaminopimelate epimerase Deposited 2007-06-12 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–274（274 aa）
Mutation：C73S TLA L(+)-TARTARIC ACID × 1 ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.8 M potassium sodium tartrate tetrahydrate, 0.2 M NaCl, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.240
2Q9J Crystal structure of the C217S mutant of diaminopimelate epimerase Deposited 2007-06-12 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–274（274 aa）
Mutation：C217S Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；(0.8 M potassium sodium tartrate tetrahydrate, 0.2 M NaCl, 0.1M HEPES), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.253

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DAPF_HAEIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–274； UniProt 1–274

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 2gkj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2gkj
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id2gkj
Deposition date deposition_date2006-04-02
Structure title titleCrystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor DL-AZIDAP
Keywords keywordsenzyme-inhibitor complex, covalently bound inhibitor, Isomerase; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier18.97 Å
Radius of gyration Rg (electron density) rg_electron18.09 Å
Forward intensity I(0) i016900200.00
Molecular weight molecular_weight30566.0 kDa
Excluded volume excluded_volume38022 ų
Envelope volume envelope_volume42767 ų
Hydration-shell volume shell_volume19367 ų
Envelope diameter envelope_diameter59.8 Å
Shell Rg shell_rg24.80 Å
Envelope Rg envelope_rg18.56 Å
Shape Rg shape_rg18.11 Å
Total Rg total_rg18.97 Å
Total atoms total_atoms2144
Residues n_residues274
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax60.5 Å
Rg (real space) rg_real18.87 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real1.6900e+07
I(0) uncertainty (real space) i0_real_error2.1600e+05
Rg (reciprocal space) rg_reciprocal18.89 Å
I(0) (reciprocal space) i0_reciprocal16900000.0000
Solution quality estimate total_estimate0.8145
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.5 Å
Skewness Skewness skewness0.232
Kurtosis Kurtosis kurtosis-0.385
Angular range angular_range— – 0.4200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6542000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.864; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2gkja1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamilyd.21.1 — Diaminopimelate epimerase-like
Family Family familyd.21.1.1 — Diaminopimelate epimerase
Domain ID domain_idd2gkja2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamilyd.21.1 — Diaminopimelate epimerase-like
Family Family familyd.21.1.1 — Diaminopimelate epimerase

CATH v4.4 (2 domains)

Domain ID domain_id2gkjA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Diaminopimelate Epimerase; Chain A, domain 1
Domain ID domain_id2gkjA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Diaminopimelate Epimerase; Chain A, domain 1
▶

8. Citations (1)

▶

9. Files and Curves (10)