1d1t

MUTANT OF HUMAN SIGMA ALCOHOL DEHYDROGENASE WITH LEUCINE AT POSITION 141

Method: X-RAY DIFFRACTION D_max: 147.1 Å Quality: REASONABLE

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

ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN

Homo sapiens

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–374 Chain B； UniProt 2–374 Chain C； UniProt 2–374 Chain D； UniProt 2–374	Mutation：M141L	ZN ZINC ION × 19 ACT ACETATE ION × 13 CAC CACODYLATE ION × 5 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM Cacodylate, pH 6.5, 100 mM Zinc Acetate, 7.5 mM NAD+, 18% PEG 6000, 8 mg/ml enzyme, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.40 Å R-free 0.274
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 2–374 Chain D； UniProt 2–374	Mutation：M141L	ZN ZINC ION × 10 ACT ACETATE ION × 7 CAC CACODYLATE ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM Cacodylate, pH 6.5, 100 mM Zinc Acetate, 7.5 mM NAD+, 18% PEG 6000, 8 mg/ml enzyme, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.40 Å R-free 0.274
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–374 Chain B； UniProt 2–374	Mutation：M141L	ZN ZINC ION × 11 ACT ACETATE ION × 6 CAC CACODYLATE ION × 5 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM Cacodylate, pH 6.5, 100 mM Zinc Acetate, 7.5 mM NAD+, 18% PEG 6000, 8 mg/ml enzyme, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.40 Å R-free 0.274
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 2–374 Chain D； UniProt 2–374	Mutation：M141L	ZN ZINC ION × 8 ACT ACETATE ION × 7 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM Cacodylate, pH 6.5, 100 mM Zinc Acetate, 7.5 mM NAD+, 18% PEG 6000, 8 mg/ml enzyme, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.40 Å R-free 0.274

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 1D1T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AGN X-RAY STRUCTURE OF HUMAN SIGMA ALCOHOL DEHYDROGENASE Deposited 1996-06-04	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–374（373 aa） Chain B 2–374（373 aa）	Not recorded	ZN ZINC ION × 8 ACT ACETATE ION × 7 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.305
1AGN X-RAY STRUCTURE OF HUMAN SIGMA ALCOHOL DEHYDROGENASE Deposited 1996-06-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–374（373 aa） Chain D 2–374（373 aa）	Not recorded	ZN ZINC ION × 8 ACT ACETATE ION × 3 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.305
1AGN X-RAY STRUCTURE OF HUMAN SIGMA ALCOHOL DEHYDROGENASE Deposited 1996-06-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–374（373 aa） Chain B 2–374（373 aa） Chain C 2–374（373 aa） Chain D 2–374（373 aa）	Not recorded	ZN ZINC ION × 16 ACT ACETATE ION × 10 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.305
1AGN X-RAY STRUCTURE OF HUMAN SIGMA ALCOHOL DEHYDROGENASE Deposited 1996-06-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–374（373 aa） Chain B 2–374（373 aa） Chain C 2–374（373 aa） Chain D 2–374（373 aa）	Not recorded	ZN ZINC ION × 16 ACT ACETATE ION × 10 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.305
1D1S WILD-TYPE HUMAN SIGMA (CLASS IV) ALCOHOL DEHYDROGENASE Deposited 1999-09-21	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–374（373 aa） Chain B 2–374（373 aa） Chain C 2–374（373 aa） Chain D 2–374（373 aa）	Not recorded	ZN ZINC ION × 19 ACT ACETATE ION × 13 CAC CACODYLATE ION × 5 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 MM CACODYLATE, 100 MM ZINC ACETATE, 7.5 MM NAD+, 18% POLYETHYLENE GLYCOL 6000, 8 MG/ML ENZYME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.50 Å R-free 0.268
1D1S WILD-TYPE HUMAN SIGMA (CLASS IV) ALCOHOL DEHYDROGENASE Deposited 1999-09-21	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 2–374（373 aa） Chain D 2–374（373 aa）	Not recorded	ZN ZINC ION × 10 ACT ACETATE ION × 7 CAC CACODYLATE ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 MM CACODYLATE, 100 MM ZINC ACETATE, 7.5 MM NAD+, 18% POLYETHYLENE GLYCOL 6000, 8 MG/ML ENZYME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.50 Å R-free 0.268
1D1S WILD-TYPE HUMAN SIGMA (CLASS IV) ALCOHOL DEHYDROGENASE Deposited 1999-09-21	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–374（373 aa） Chain B 2–374（373 aa）	Not recorded	ZN ZINC ION × 11 ACT ACETATE ION × 6 CAC CACODYLATE ION × 5 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 MM CACODYLATE, 100 MM ZINC ACETATE, 7.5 MM NAD+, 18% POLYETHYLENE GLYCOL 6000, 8 MG/ML ENZYME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.50 Å R-free 0.268
1D1S WILD-TYPE HUMAN SIGMA (CLASS IV) ALCOHOL DEHYDROGENASE Deposited 1999-09-21	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–374（373 aa） Chain D 2–374（373 aa）	Not recorded	ZN ZINC ION × 8 ACT ACETATE ION × 7 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 MM CACODYLATE, 100 MM ZINC ACETATE, 7.5 MM NAD+, 18% POLYETHYLENE GLYCOL 6000, 8 MG/ML ENZYME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.50 Å R-free 0.268

2 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ADH7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–373； UniProt 2–374 Author chain B； PDBConstruct 2–373； UniProt 2–374 Author chain C； PDBConstruct 2–373； UniProt 2–374 Author chain D； PDBConstruct 2–373； UniProt 2–374

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1d1t
Deposition date deposition_date	1999-09-21
Structure title title	MUTANT OF HUMAN SIGMA ALCOHOL DEHYDROGENASE WITH LEUCINE AT POSITION 141
Keywords keywords	ROSSMANN OR DINUCLEOTIDE FOLD, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	42.90 Å
Radius of gyration Rg (electron density) rg_electron	43.54 Å
Forward intensity I(0) i0	406499000.00
Molecular weight molecular_weight	164790.0 kDa
Excluded volume excluded_volume	206000 Å³
Envelope volume envelope_volume	258670 Å³
Hydration-shell volume shell_volume	52611 Å³
Envelope diameter envelope_diameter	159.9 Å
Shell Rg shell_rg	44.51 Å
Envelope Rg envelope_rg	43.45 Å
Shape Rg shape_rg	43.56 Å
Total Rg total_rg	43.52 Å
Total atoms total_atoms	11428
Residues n_residues	1492
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	147.1 Å
Rg (real space) rg_real	43.25 Å
Rg uncertainty (real space) rg_real_error	1.70 Å
I(0) (real space) i0_real	4.0650e+08
I(0) uncertainty (real space) i0_real_error	8.0410e+06
Rg (reciprocal space) rg_reciprocal	42.90 Å
I(0) (reciprocal space) i0_reciprocal	406300000.0000
Solution quality estimate total_estimate	0.6122
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.8 Å
Skewness Skewness skewness	0.526
Kurtosis Kurtosis kurtosis	-0.294
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	63390000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.789; Stabil: 1.000; Sysdev: 0.083; Positv: 1.000; Valcen: 0.830; Smooth: 0.507

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN
Molecular weight formula_weight	39906.3 kDa
EC 编号 ec_number	1.1.1.1
Mutation mutation	M141L
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11799

GTAGKVIKCKAAVLWEQKQPFSIEEIEVAPPKTKEVRIKILATGICRTDDHVIKGTMVSKFPVIVGHEATGIVESIGEGVTTVKPGDKVIPLFLPQCRECNACRNPDGNLCIRSDITGRGVLADGTTRFTCKGKPVHHFLNTSTFTEYTVVDESSVAKIDDAAPPEKVCLIGCGFSTGYGAAVKTGKVKPGSTCVVFGLGGVGLSVIMGCKSAGASRIIGIDLNKDKFEKAMAVGATECISPKDSTKPISEVLSEMTGNNVGYTFEVIGHLETMIDALASCHMNYGTSVVVGVPPSAKMLTYDPMLLFTGRTWKGCVFGGLKSRDDVPKLVTEFLAKKFDLDQLITHVLPFKKISEGFELLNSGQSIRTVLTF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	19

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 4 Entity 4 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	371

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1d1ta1
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1d1ta2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1d1tb1
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1d1tb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1d1tc1
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1d1tc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1d1td1
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1d1td2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id	1d1tA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

Domain ID domain_id	1d1tA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1d1tB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

Domain ID domain_id	1d1tB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1d1tC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

Domain ID domain_id	1d1tC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1d1tD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

Domain ID domain_id	1d1tD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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8. Citations (2)

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Unit-cell length a length_a	85.900 Å
Unit-cell length b length_b	90.500 Å
Unit-cell length c length_c	119.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2210
R_work r_work	0.2160
R_free r_free	0.2740

fit	/app/data/saxs_computation/d1/1d1t/1d1t.fit
pddf	/app/data/pr_computation/d1/1d1t/1d1t.pr.out
profile	/app/data/saxs_computation/d1/1d1t/1d1t.dat