SAXSdb — 1g5q

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

EPIDERMIN MODIFYING ENZYME EPID

Staphylococcus epidermidis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	LANTIBIOTIC EPIDERMIN × 12 （P08136） FLAVIN MONONUCLEOTIDE × 12 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 6 water × 18	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EPID_STAEP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–181； UniProt 1–181 Author chain D； PDBConstruct 1–181； UniProt 1–181 Author chain G； PDBConstruct 1–181； UniProt 1–181 Author chain L； PDBConstruct 1–181； UniProt 1–181

LANTIBIOTIC EPIDERMIN

OrganismNot specified

UniProt P08136

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	EPIDERMIN MODIFYING ENZYME EPID × 12 （P30197） FLAVIN MONONUCLEOTIDE × 12 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 6 water × 18	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LANE_STAEP
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–5； UniProt 48–52 Author chain N； PDBConstruct 1–5； UniProt 48–52 Author chain O； PDBConstruct 1–5； UniProt 48–52 Author chain P； PDBConstruct 1–5； UniProt 48–52

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1g5q
Deposition date deposition_date	2000-11-02
Structure title title	EPID H67N COMPLEXED WITH SUBSTRATE PEPTIDE DSYTC
Keywords keywords	alpha, beta protein, Rossman like fold, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1g5q__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1g5q__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1g5q__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	39.59 Å
Rg (electron density)	38.38 Å
Total Rg	38.76 Å
Atom count	17712
Residues	2148
Excluded volume	318070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1g5q__assembly_1__model_1`	24-meric （24）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	EPIDERMIN MODIFYING ENZYME EPID
Molecular weight formula_weight	20821.0 kDa
Mutation mutation	H67N
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,L
Atom count atom_count	6040

MYGKLLICATASINVININHYIVELKQHFDEVNILFSPSSKNFINTDVLKLFCDNLYDEIKDPLLNNINIVENHEYILVLPASANTINKIANGICDNLLTTVCLTGYQKLFIFPNMNIRMWGNPFLQKNIDLLKNNDVKVYSPDMNKSFEISSGRYKNNITMPNIENVLNFVLNNEKRPLD

Source Source

Source organism organism	Staphylococcus epidermidis
NCBI taxonomy ID ncbi_taxonomy_id	1282
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	LANTIBIOTIC EPIDERMIN
Molecular weight formula_weight	587.6 kDa
Mutation mutation	N401D C404T
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O,P

DSYTC

Entity 3 Entity 3 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	136

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1g5qa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.34 — Homo-oligomeric flavin-containing Cys decarboxylases, HFCD
Superfamily Superfamily superfamily	c.34.1 — Homo-oligomeric flavin-containing Cys decarboxylases, HFCD
Family Family family	c.34.1.1 — Homo-oligomeric flavin-containing Cys decarboxylases, HFCD

Domain ID domain_id	d1g5qd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.34 — Homo-oligomeric flavin-containing Cys decarboxylases, HFCD
Superfamily Superfamily superfamily	c.34.1 — Homo-oligomeric flavin-containing Cys decarboxylases, HFCD
Family Family family	c.34.1.1 — Homo-oligomeric flavin-containing Cys decarboxylases, HFCD

Domain ID domain_id	d1g5qg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.34 — Homo-oligomeric flavin-containing Cys decarboxylases, HFCD
Superfamily Superfamily superfamily	c.34.1 — Homo-oligomeric flavin-containing Cys decarboxylases, HFCD
Family Family family	c.34.1.1 — Homo-oligomeric flavin-containing Cys decarboxylases, HFCD

Domain ID domain_id	d1g5ql_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.34 — Homo-oligomeric flavin-containing Cys decarboxylases, HFCD
Superfamily Superfamily superfamily	c.34.1 — Homo-oligomeric flavin-containing Cys decarboxylases, HFCD
Family Family family	c.34.1.1 — Homo-oligomeric flavin-containing Cys decarboxylases, HFCD

CATH v4.4 (4 domains)

Domain ID domain_id	1g5qA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1950 — Flavin prenyltransferase-like

Domain ID domain_id	1g5qD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1950 — Flavin prenyltransferase-like

Domain ID domain_id	1g5qG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1950 — Flavin prenyltransferase-like

Domain ID domain_id	1g5qL00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1950 — Flavin prenyltransferase-like

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Unit-cell length a length_a	223.552 Å
Unit-cell length b length_b	223.552 Å
Unit-cell length c length_c	223.552 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	96

Space group space_group	I 21 3
Space-group number int_tables_number	199
Crystal system crystal_system	—

Resolution resolution	2.570 Å
Low-resolution limit resolution_low	19.920 Å
R factor r_factor	—
R_work r_work	0.2090
R_free r_free	0.2260

EPID H67N COMPLEXED WITH SUBSTRATE PEPTIDE DSYTC

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

EPIDERMIN MODIFYING ENZYME EPID

State in the Current Structure

Other States of the Same Protein in the Database

LANTIBIOTIC EPIDERMIN

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1g5q__assembly_1__model_1

1g5q__assembly_1__model_1 | I(q)

1g5q__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)

EPID H67N COMPLEXED WITH SUBSTRATE PEPTIDE DSYTC

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

EPIDERMIN MODIFYING ENZYME EPID

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

LANTIBIOTIC EPIDERMIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1g5q__assembly_1__model_1

1g5q__assembly_1__model_1 | I(q)

1g5q__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)