1npy

Structure of shikimate 5-dehydrogenase-like protein HI0607

Method: X-RAY DIFFRACTION

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

Hypothetical shikimate 5-dehydrogenase-like protein HI0607

Haemophilus influenzae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ACETYL GROUP × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ACETYL GROUP × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ACETYL GROUP × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y607_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–271； UniProt 1–271 Author chain B； PDBConstruct 1–271； UniProt 1–271 Author chain C； PDBConstruct 1–271； UniProt 1–271 Author chain D； PDBConstruct 1–271； UniProt 1–271

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	1npy
Deposition date deposition_date	2003-01-20
Structure title title	Structure of shikimate 5-dehydrogenase-like protein HI0607
Keywords keywords	STRUCTURAL GENOMICS, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

1npy__assembly_1__model_1

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

Download this curve (.dat)

1npy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1npy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.48 Å
Rg (electron density)	19.43 Å
Total Rg	20.32 Å
Atom count	2087
Residues	269
Excluded volume	37421 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1npy__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1npy__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1npy__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1npy__assembly_4__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	Hypothetical shikimate 5-dehydrogenase-like protein HI0607
Molecular weight formula_weight	29966.4 kDa
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	9521

MINKDTQLCMSLSGRPSNFGTTFHNYLYDKLGLNFIYKAFTTQDIEHAIKGVRALGIRGCAVSMPFKETCMPFLDEIHPSAQAIESVNTIVNDNGFLRAYNTDYIAIVKLIEKYHLNKNAKVIVHGSGGMAKAVVAAFKNSGFEKLKIYARNVKTGQYLAALYGYAYINSLENQQADILVNVTSIGMKGGKEEMDLAFPKAFIDNASVAFDVVAMPVETPFIRYAQARGKQTISGAAVIVLQAVEQFELYTHQRPSDELIAEAAAFARTKF

Source Source

Source organism organism	Haemophilus influenzae
NCBI taxonomy ID ncbi_taxonomy_id	727
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETYL GROUP
Molecular weight formula_weight	44.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1149

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1npya1
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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1npya2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.5 — Shikimate dehydrogenase-like

Domain ID domain_id	d1npyb1
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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1npyb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.5 — Shikimate dehydrogenase-like

Domain ID domain_id	d1npyc1
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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1npyc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.5 — Shikimate dehydrogenase-like

Domain ID domain_id	d1npyd1
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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1npyd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.5 — Shikimate dehydrogenase-like

CATH v4.4 (8 domains)

Domain ID domain_id	1npyA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	1npyA02
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	1npyB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	1npyB02
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	1npyC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	1npyC02
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	1npyD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	1npyD02
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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Unit-cell length a length_a	90.578 Å
Unit-cell length b length_b	66.575 Å
Unit-cell length c length_c	96.916 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.56 °
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	1.750 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1813
R_work r_work	0.1793
R_free r_free	0.2191

Structure of shikimate 5-dehydrogenase-like protein HI0607

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

Hypothetical shikimate 5-dehydrogenase-like protein HI0607

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

1npy__assembly_1__model_1

1npy__assembly_1__model_1 | I(q)

1npy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of shikimate 5-dehydrogenase-like protein HI0607

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

Hypothetical shikimate 5-dehydrogenase-like protein HI0607

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

1npy__assembly_1__model_1

1npy__assembly_1__model_1 | I(q)

1npy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)