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1c6z

ALTERNATE BINDING SITE FOR THE P1-P3 GROUP OF A CLASS OF POTENT HIV-1 PROTEASE INHIBITORS AS A RESULT OF CONCERTED STRUCTURAL CHANGE IN 80'S LOOP.

Method: X-RAY DIFFRACTION Dmax: 65.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (PROTEASE)

Human immunodeficiency virus 1

UniProt O09893

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–99 Chain B； UniProt 1–99 Not recorded ROC (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions：CRYSTALS OBTAINED BY CO-CRYSTALLIZATION AT PH 5.2, USING 0.6M NaCl AS PRECIPITATING AGENT IN 0.1M SODIUM ACETATE BUFFER. PROTEIN WAS AT 5.5 MG/ML CONCENTRATION. Resolution 2.50 Å R-free 0.290

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 1C6Z Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C6X ALTERNATE BINDING SITE FOR THE P1-P3 GROUP OF A CLASS OF POTENT HIV-1 PROTEASE INHIBITORS AS A RESULT OF CONCERTED STRUCTURAL CHANGE IN 80'S LOOP. Deposited 1999-12-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–99（99 aa）
Chain B 1–99（99 aa）
Not recorded 3IN N-[2(S)-CYCLOPENTYL-1(R)-HYDROXY-3(R)METHYL]-5-[(2(S)-TERTIARY-BUTYLAMINO-CARBONYL)-4-(N1-(2)-(N-METHYLPIPERAZINYL)-3-CHLORO-PYRAZINYL-5-CARBONYL)-PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYL-PENTANAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions crystals obtained by co-crystallization at ph 5.2, using 0.6M NaCl as precipitating agent in 0.1M sodium acetate buffer. protein was at 5.5 mg/ml concentration
Resolution 2.50 Å R-free 0.300
1C6Y ALTERNATE BINDING SITE FOR THE P1-P3 GROUP OF A CLASS OF POTENT HIV-1 PROTEASE INHIBITORS AS A RESULT OF CONCERTED STRUCTURAL CHANGE IN 80'S LOOP. Deposited 1999-12-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–99（99 aa）
Chain B 1–99（99 aa）
Not recorded MK1 N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions THE CRYSTAL WAS PREPARED WITH CO CRYSTALLIZATION METHOD. 9X MUTANT PROTEASE HAS NINE POINT MUTATIONS COMPARED TO WILD TYPE: L10V,K20M,L24I,S37D,M46I,I54V,L63P,A71V,V82T THERE IS ONE PROTEASE DIMER IN AN ASYMMETRICAL UNIT. THE TWO MOLECULES ARE LABELED AS CHAIN A AND CHAIN B. THERE IS ONE L-735,524 INHIBITOR MOLECULE LABELED AS MK1.
Resolution 2.50 Å R-free 0.310

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name O09893_9HIV1
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–99； UniProt 1–99 Author chain B； PDBConstruct 1–99； UniProt 1–99

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 1c6z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1c6z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1c6z
Deposition date deposition_date1999-12-28
Structure title titleALTERNATE BINDING SITE FOR THE P1-P3 GROUP OF A CLASS OF POTENT HIV-1 PROTEASE INHIBITORS AS A RESULT OF CONCERTED STRUCTURAL CHANGE IN 80'S LOOP.
Keywords keywordshydrolase-hydrolase inhibitor complex; HYDROLASE/HYDROLASE INHIBITOR
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_guinier18.25 Å
Radius of gyration Rg (electron density) rg_electron17.31 Å
Forward intensity I(0) i07977000.00
Molecular weight molecular_weight22220.0 kDa
Excluded volume excluded_volume28494 ų
Envelope volume envelope_volume32025 ų
Hydration-shell volume shell_volume15906 ų
Envelope diameter envelope_diameter62.1 Å
Shell Rg shell_rg22.90 Å
Envelope Rg envelope_rg17.56 Å
Shape Rg shape_rg17.31 Å
Total Rg total_rg18.26 Å
Total atoms total_atoms1563
Residues n_residues198
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 dmax65.0 Å
Rg (real space) rg_real18.23 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real7.9770e+06
I(0) uncertainty (real space) i0_real_error1.0600e+05
Rg (reciprocal space) rg_reciprocal18.23 Å
I(0) (reciprocal space) i0_reciprocal7977000.0000
Solution quality estimate total_estimate0.7585
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary59.7 Å
Skewness Skewness skewness0.354
Kurtosis Kurtosis kurtosis-0.236
Angular range angular_range— – 0.4350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3268000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.639; Stabil: 0.989; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1c6za_
Class classb — All beta proteins
Fold Fold foldb.50 — Acid proteases
Superfamily Superfamily superfamilyb.50.1 — Acid proteases
Family Family familyb.50.1.1 — Retroviral protease (retropepsin)
Domain ID domain_idd1c6zb_
Class classb — All beta proteins
Fold Fold foldb.50 — Acid proteases
Superfamily Superfamily superfamilyb.50.1 — Acid proteases
Family Family familyb.50.1.1 — Retroviral protease (retropepsin)

CATH v4.4 (2 domains)

Domain ID domain_id1c6zA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acid Proteases
Domain ID domain_id1c6zB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acid Proteases
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8. Citations (2)

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9. Files and Curves (10)