SAXSdb — 6z2w

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

DNA damage checkpoint protein LCD1

Saccharomyces cerevisiae S288C

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Serine/threonine-protein kinase MEC1 × 2 （P38111） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 ZINC ION × 2 MAGNESIUM ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LCD1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–747； UniProt 1–747 Author chain D； PDBConstruct 1–747； UniProt 1–747

Serine/threonine-protein kinase MEC1

Saccharomyces cerevisiae S288C

UniProt P38111

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA damage checkpoint protein LCD1 × 2 （Q04377） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 ZINC ION × 2 MAGNESIUM ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATR_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–2368； UniProt 1–2368 Author chain F； PDBConstruct 1–2368； UniProt 1–2368

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	6z2w
Deposition date deposition_date	2020-05-18
Structure title title	Mec1-Ddc2 (F2244L mutant) in complex with Mg AMP-PNP
Keywords keywords	serine/threonine protein kinase, complex, DNA damage response, checkpoint control, Hydrolase; HYDROLASE
Experimental Method method	ELECTRON MICROSCOPY

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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.

6z2w__assembly_1__model_1

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

Download this curve (.dat)

6z2w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6z2w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	64.90 Å
Rg (electron density)	64.50 Å
Total Rg	64.65 Å
Atom count	46562
Residues	5766
Excluded volume	836890 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6z2w__assembly_1__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	DNA damage checkpoint protein LCD1
Molecular weight formula_weight	86533.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,C
Atom count atom_count	46588

MRRETVGEFSSDDDDDILLELGTRPPRFTQIPPSSAALQTQIPTTLEVTTTTLNNKQSKNDNQLVNQLNKAQGEASMLRDKINFLNIEREKEKNIQAVKVNELQVKHLQELAKLKQELQKLEDEKKFLQMEARGKSKREVITNVKPPSTTLSTNTNTITPDSSSVAIEAKPQSPQSKKRKISDNLLKKNMVPLNPNRIIPDETSLFLESILLHQIIGADLSTIEILNRLKLDYITEFKFKNFVIAKGAPIGKSIVSLLLRCKKTLTLDRFIDTLLEDIAVLIKEISVHPNESKLAVPFLVALMYQIVQFRPSATHNLALKDCFLFICDLIRIYHHVLKVPIHESNMNLHVEPQIFQYELIDYLIISYSFDLLEGILRVLQSHPKQTYMEFFDENILKSFEFVYKLALTISYKPMVNVIFSAVEVVNIITSIILNMDNSSDLKSLISGSWWRDCITRLYALLEKEIKSGDVYNENVDTTTLHMSKYHDFFGLIRNIGDNELGGLISKLIYTDRLQSVPRVISKEDIGMDSDKFTAPIIGYKMEKWLLKLKDEVLNIFENLLMIYGDDATIVNGEMLIHSSKFLSREQALMIERYVGQDSPNLDLRCHLIEHTLTIIYRLWKDHFKQLREEQIKQVESQLIMSLWRFLVCQTETVTANEREMRDHRHLVDSLHDLTIKDQASYYEDAFEDLPEYIEEELKMQLNKRTGRIMQVKYDEKFQEMARTILESKSFDLTTLEEADSLYISMGL

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	Serine/threonine-protein kinase MEC1
Molecular weight formula_weight	273646.8 kDa
EC 编号 ec_number	2.7.11.1
Mutation mutation	F2244L
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

MESHVKYLDELILAIKDLNSGVDSKVQIKKVPTDPSSSQEYAKSLKILNTLIRNLKDQRRNNIMKNDTIFSKTVSALALLLEYNPFLLVMKDSNGNFEIQRLIDDFLNISVLNYDNYHRIWFMRRKLGSWCKACVEFYGKPAKFQLTAHFENTMNLYEQALTEVLLGKTELLKFYDTLKGLYILLYWFTSEYSTFGNSIAFLDSSLGFTKFDFNFQRLIRIVLYVFDSCELAALEYAEIQLKYISLVVDYVCNRTISTALDAPALVCCEQLKFVLTTMHHFLDNKYGLLDNDPTMAKGILRLYSLCISNDFSKCFVDHFPIDQWADFSQSEHFPFTQLTNKALSIVYFDLKRRSLPVEALKYDNKFNIWVYQSEPDSSLKNVTSPFDDRYKQLEKLRLLVLKKFNKTERGTLLKYRVNQLSPGFFQRAGNDFKLILNEASVSIQTCFKTNNITRLTSWTVILGRLACLESEKFSGTLPNSTKDMDNWYVCHLCDIEKTGNPFVRINPNRPEAAGKSEIFRILHSNFLSHPNIDEFSESLLSGILFSLHRIFSHFQPPKLTDGNGQINKSFKLVQKCFMNSNRYLRLLSTRIIPLFNISDSHNSEDEHTATLIKFLQSQKLPVVKENLVIAWTQLTLTTSNDVFDTLLLKLIDIFNSDDYSLRIMMTLQIKNMAKILKKTPYQLLSPILPVLLRQLGKNLVERKVGFQNLIELLGYSSKTILDIFQRYIIPYAIIQYKSDVLSEIAKIMCDGDTSLINQMKVNLLKKNSRQIFAVALVKHGLFSLDILETLFLNRAPTFDKGYITAYLPDYKTLAEITKLYKNSVTKDASDSENANMILCSLRFLITNFEKDKRHGSKYKNINNWTDDQEQAFQKKLQDNILGIFQVFSSDIHDVEGRTTYYEKLRVINGISFLIIYAPKKSIISALAQISICLQTGLGLKEVRYEAFRCWHLLVRHLNDEELSTVIDSLIAFILQKWSEFNGKLRNIVYSILDTLIKEKSDLILKLKPYTTLALVGKPELGILARDGQFARMVNKIRSTTDLIPIFANNLKSSNKYVINQNLDDIEVYLRRKQTERSIDFTPKKVGQTSDITLVLGALLDTSHKFRNLDKDLCEKCAKCISMIGVLDVTKHEFKRTTYSENEVYDLNDSVQTIKFLIWVINDILVPAFWQSENPSKQLFVALVIQESLKYCGLSSESWDMNHKELYPNEAKLWEKFNSVSKTTIYPLLSSLYLAQSWKEYVPLKYPSNNFKEGYKIWVKRFTLDLLKTGTTENHPLHVFSSLIREDDGSLSNFLLPYISLDIIIKAEKGTPYADILNGIIIEFDSIFTCNLEGMNNLQVDSLRMCYESIFRVFEYCKKWATEFKQNYSKLHGTFIIKDTKTTNMLLRIDEFLRTTPSDLLAQRSLETDSFERSALYLEQCYRQNPHDKNQNGQLLKNLQITYEEIGDIDSLDGVLRTFATGNLVSKIEELQYSENWKLAQDCFNVLGKFSDDPKTTTRMLKSMYDHQLYSQIISNSSFHSSDGKISLSPDVKEWYSIGLEAANLEGNVQTLKNWVEQIESLRNIDDREVLLQYNIAKALIAISNEDPLRTQKYIHNSFRLIGTNFITSSKETTLLKKQNLLMKLHSLYDLSFLSSAKDKFEYKSNTTILDYRMERIGADFVPNHYILSMRKSFDQLKMNEQADADLGKTFFTLAQLARNNARLDIASESLMHCLERRLPQAELEFAEILWKQGENDRALKIVQEIHEKYQENSSVNARDRAAVLLKFTEWLDLSNNSASEQIIKQYQDIFQIDSKWDKPYYSIGLYYSRLLERKKAEGYITNGRFEYRAISYFLLAFEKNTAKVRENLPKVITFWLDIAAASISEAPGNRKEMLSKATEDICSHVEEALQHCPTYIWYFVLTQLLSRLLHSHQSSAQIIMHILLSLAVEYPSHILWYITALVNSNSSKRVLRGKHILEKYRQHSQNPHDLVSSALDLTKALTRVCLQDVKSITSRSGKSLEKDFKFDMNVAPSAMVVPVRKNLDIISPLESNSMRGYQPFRPVVSIIRFGSSYKVFSSLKKPKQLNIIGSDGNIYGIMCKKEDVRQDNQYMQFATTMDFLLSKDIASRKRSLGINIYSVLSLREDCGILEMVPNVVTLRSILSTKYESLKIKYSLKSLHDRWQHTAVDGKLEFYMEQVDKFPPILYQWFLENFPDPINWFNARNTYARSYAVMAMVGHILGLGDRHCENILLDIQTGKVLHVDLDCLFEKGKRLPVPEIVPFRLTPNLLDALGIIGTEGTFKKSSEVTLALMRKNEVALMNVIETIMYDRNMDHSIQKALKVLRNKIRGIDPQDGLVLSVAGQTETLIQEATSEDNLSKMYIGWLPFW

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 3 Entity 3 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	4

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.82 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	53581

Mec1-Ddc2 (F2244L mutant) in complex with Mg AMP-PNP

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

DNA damage checkpoint protein LCD1

State in the Current Structure

Other States of the Same Protein in the Database

Serine/threonine-protein kinase MEC1

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

6z2w__assembly_1__model_1

6z2w__assembly_1__model_1 | I(q)

6z2w__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Mec1-Ddc2 (F2244L mutant) in complex with Mg AMP-PNP

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

DNA damage checkpoint protein LCD1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Serine/threonine-protein kinase MEC1

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

6z2w__assembly_1__model_1

6z2w__assembly_1__model_1 | I(q)

6z2w__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)