SAXSdb — 1w1t

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

CHITINASE B

SERRATIA MARCESCENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 19 SULFATE ION × 6 CYCLO-(L-HISTIDINE-L-PROLINE) INHIBITOR × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q54276_SERMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–499； UniProt 1–499 Author chain B； PDBConstruct 1–499； UniProt 1–499

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	1w1t
Deposition date deposition_date	2004-06-24
Structure title title	Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide inhibitor cyclo-(His-L-Pro) at 1.9 A resolution
Keywords keywords	HYDROLASE, GLYCOSIDE HYDROLASE, CHITINASE, STRUCTURE-BASED INHIBITOR DESIGN, CYCLIC DIPEPTIDE; HYDROLASE
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.

1w1t__assembly_1__model_1

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

Download this curve (.dat)

1w1t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1w1t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.77 Å
Rg (electron density)	36.26 Å
Total Rg	36.67 Å
Atom count	8015
Residues	994
Excluded volume	141560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1w1t__assembly_1__model_1`	dimeric （2）	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	CHITINASE B
Molecular weight formula_weight	55518.0 kDa
EC 编号 ec_number	3.2.1.14
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8817

MSTRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPASRAKFAQSCVRIMKDYGFDGVDIDWEYPQAAEVDGFIAALQEIRTLLNQQTITDGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKVTNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPSTDYWLVGCEECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRVA

Source Source

Source organism organism	SERRATIA MARCESCENS
NCBI taxonomy ID ncbi_taxonomy_id	615
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	19

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	CYCLO-(L-HISTIDINE-L-PROLINE) INHIBITOR
Molecular weight formula_weight	234.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	780

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1w1ta1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.5 — Type II chitinase

Domain ID domain_id	d1w1ta2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.3 — Chitinase insertion domain
Family Family family	d.26.3.1 — Chitinase insertion domain

Domain ID domain_id	d1w1ta3
Class class	b — All beta proteins
Fold Fold fold	b.72 — WW domain-like
Superfamily Superfamily superfamily	b.72.2 — Carbohydrate binding domain
Family Family family	b.72.2.1 — Carbohydrate binding domain

Domain ID domain_id	d1w1tb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.5 — Type II chitinase

Domain ID domain_id	d1w1tb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.3 — Chitinase insertion domain
Family Family family	d.26.3.1 — Chitinase insertion domain

Domain ID domain_id	d1w1tb3
Class class	b — All beta proteins
Fold Fold fold	b.72 — WW domain-like
Superfamily Superfamily superfamily	b.72.2 — Carbohydrate binding domain
Family Family family	b.72.2.1 — Carbohydrate binding domain

CATH v4.4 (6 domains)

Domain ID domain_id	1w1tA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	1w1tA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1w1tA03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	20 — Carbohydrate-binding module superfamily 5/12

Domain ID domain_id	1w1tB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	1w1tB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1w1tB03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	20 — Carbohydrate-binding module superfamily 5/12

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Unit-cell length a length_a	55.845 Å
Unit-cell length b length_b	103.975 Å
Unit-cell length c length_c	186.016 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	24.880 Å
R factor r_factor	0.1930
R_work r_work	0.1930
R_free r_free	0.2220

Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide inhibitor cyclo-(His-L-Pro) at 1.9 A resolution

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

CHITINASE B

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

1w1t__assembly_1__model_1

1w1t__assembly_1__model_1 | I(q)

1w1t__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide inhibitor cyclo-(His-L-Pro) at 1.9 A resolution

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

CHITINASE B

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

1w1t__assembly_1__model_1

1w1t__assembly_1__model_1 | I(q)

1w1t__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)