3fsy

Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c;DapD) in complex with succinyl-CoA from Mycobacterium tuberculosis

Method: X-RAY DIFFRACTION

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

Tetrahydrodipicolinate N-succinyltransferase

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	SUCCINYL-COENZYME A × 3 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 MAGNESIUM ION × 5 SODIUM ION × 2 ACETIC ACID × 2 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	(4S)-2-METHYL-2,4-PENTANEDIOL × 3 MAGNESIUM ION × 6 SODIUM ION × 3 ACETIC ACID × 3 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	SUCCINYL-COENZYME A × 3 MAGNESIUM ION × 9 SODIUM ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O05302_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–319； UniProt 2–317 Author chain B； PDBConstruct 4–319； UniProt 2–317 Author chain C； PDBConstruct 4–319； UniProt 2–317 Author chain D； PDBConstruct 4–319； UniProt 2–317 Author chain E； PDBConstruct 4–319； UniProt 2–317

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	3fsy
Deposition date deposition_date	2009-01-12
Structure title title	Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c;DapD) in complex with succinyl-CoA from Mycobacterium tuberculosis
Keywords keywords	beta helix, L beta H domain, Acyltransferase, TRANSFERASE; TRANSFERASE
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.

3fsy__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3fsy__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fsy__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.45 Å
Rg (electron density)	27.34 Å
Total Rg	28.22 Å
Atom count	6702
Residues	924
Excluded volume	118640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fsy__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fsy__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3fsy__assembly_3__model_1`	trimeric （3）	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 (7)

Entity 1 Entity 1 polymer

Description description	Tetrahydrodipicolinate N-succinyltransferase
Molecular weight formula_weight	34384.7 kDa
EC 编号 ec_number	2.3.1.117
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	11992

MAVSTVTGAAGIGLATLAADGSVLDTWFPAPELTESGTSATSRLAVSDVPVELAALIGRDDDRRTETIAVRTVIGSLDDVAADPYDAYLRLHLLSHRLVAPHGLNAGGLFGVLTNVVWTNHGPCAIDGFEAVRARLRRRGPVTVYGVDKFPRMVDYVVPTGVRIADADRVRLGAHLAPGTTVMHEGFVNYNAGTLGASMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTHVISIGKRCLLGANSGLGISLGDDCVVEAGLYVTAGTRVTMPDSNSVKARELSGSSNLLFRRNSVSGAVEVLARDGQGIALNEDLHANGVPRGLEHHHHHH

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SUCCINYL-COENZYME A
Molecular weight formula_weight	867.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	737

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6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

Domain ID domain_id	3fsyA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2010 —

Domain ID domain_id	3fsyA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	70 — Trimeric LpxA-like enzymes

Domain ID domain_id	3fsyA03
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	3fsyB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2010 —

Domain ID domain_id	3fsyB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	70 — Trimeric LpxA-like enzymes

Domain ID domain_id	3fsyB03
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	3fsyC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2010 —

Domain ID domain_id	3fsyC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	70 — Trimeric LpxA-like enzymes

Domain ID domain_id	3fsyC03
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	3fsyD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2010 —

Domain ID domain_id	3fsyD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	70 — Trimeric LpxA-like enzymes

Domain ID domain_id	3fsyD03
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	3fsyE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2010 —

Domain ID domain_id	3fsyE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	70 — Trimeric LpxA-like enzymes

Domain ID domain_id	3fsyE03
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

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Unit-cell length a length_a	216.960 Å
Unit-cell length b length_b	216.960 Å
Unit-cell length c length_c	216.960 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	120

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

Resolution resolution	1.970 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1615
R_work r_work	0.1610
R_free r_free	0.1999

Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c;DapD) in complex with succinyl-CoA from Mycobacterium tuberculosis

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

Tetrahydrodipicolinate N-succinyltransferase

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

3fsy__assembly_2__model_1

3fsy__assembly_2__model_1 | I(q)

3fsy__assembly_2__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

7. Citations (1)

Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c;DapD) in complex with succinyl-CoA from Mycobacterium tuberculosis

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

Tetrahydrodipicolinate N-succinyltransferase

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

3fsy__assembly_2__model_1

3fsy__assembly_2__model_1 | I(q)

3fsy__assembly_2__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

7. Citations (1)