2DQS: PDB entry 2DQS

Crystal structure of the calcium pump with amppcp in the absence of calcium. Determined by X-ray diffraction at 2.5 Å resolution. Released 5 Jun 2007.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Oryctolagus cuniculus
Chains: 1
Atoms: 8,024
Mol. weight: 112.32 kDa
Ligands: PTY, TG1, ACP, MG
Released: 5 Jun 2007

Explore 2DQS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2DQS contains 56 α-helices and 35 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 56 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	9-16	8
β-strand	24	1	1
α-helix	26-36	11
α-helix	41-44	4
α-helix	49-54	6
α-helix	55-57	3
α-helix	60-77	18
α-helix	84-87	4
α-helix	89-110	22
α-helix	115-119	5
α-helix	120-122	3
β-strand	126-130	5	2
β-strand	131	1	1
β-strand	138-141	4	2
α-helix	142-144	3
β-strand	150-154	5	2
β-strand	158	1	3
β-strand	162-168	7	2
β-strand	173-176	4	3
α-helix	178-181	4
β-strand	187-189	3	3
α-helix	201-203	3
β-strand	207-208	2	2
β-strand	213-216	4	3
β-strand	218-225	8	2
α-helix	227-229	3
α-helix	231-241	11
α-helix	248-273	26
α-helix	276-278	3
α-helix	289-306	18
α-helix	311-327	17
β-strand	331-333	3	4
α-helix	338-343	6
β-strand	347-351	5	4
β-strand	357	1	5
β-strand	362-373	12	6
β-strand	376-384	9	6
β-strand	395-397	3	6
β-strand	400-401	2	6
α-helix	404-406	3
α-helix	408-419	12
β-strand	424-427	4	7
β-strand	434-437	4	7
α-helix	440-452	13
α-helix	464-467	4
α-helix	470-476	7
β-strand	479-488	10	6
β-strand	493-500	8	6
β-strand	511-516	6	6
α-helix	518-523	6
β-strand	525-530	6	6
β-strand	533-536	4	6
α-helix	539-554	16
β-strand	560-567	8	6
α-helix	570-572	3
α-helix	573-575	3
α-helix	581-583	3
α-helix	584-587	4
β-strand	591-600	10	6
α-helix	602	1
β-strand	603	1	5
α-helix	604	1
α-helix	607-616	10
β-strand	620-625	6	4
α-helix	629-639	11
β-strand	652-654	3	4
α-helix	655-660	6
α-helix	663-672	10
β-strand	675-677	3	4
α-helix	683-692	10
β-strand	698-702	5	4
α-helix	705-707	3
α-helix	708-713	6
β-strand	716-720	5	4
α-helix	725-729	5
β-strand	733-735	3	4
α-helix	740-780	41
α-helix	783-785	3
α-helix	789-794	6
α-helix	795-799	5
α-helix	801-807	7
α-helix	810-813	4
α-helix	821-823	3
α-helix	831-854	24
α-helix	890-892	3
α-helix	894-913	20
α-helix	927-929	3
α-helix	931-949	19
α-helix	952-956	5
α-helix	966-974	9
α-helix	976-990	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1	A	protein	995	Oryctolagus cuniculus	P04191 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2DQS_1 Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (chains A)
XMEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLWELVIEQFED
LLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEAL
KEYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSI
LTGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQM
AATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIA
VALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTN
QMSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICAL
CNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLM
KKEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTG
PVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGM
LDPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFD
DLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIA
MGSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTA
ALGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMA
IGGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTM
ALSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKL
KALDLTQWLMVLKISLPVIGLDEILKFIARNYLEG

Ligands and cofactors

ID	Name	Formula	Copies
PTY	Phosphatidylethanolamine	C40 H80 N O8 P	2
TG1	Octanoic acid [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA, 6ABETA, 7BETA, 8ALPHA(Z),…	C34 H50 O12	1
ACP	Phosphomethylphosphonic acid adenylate ester	C11 H18 N5 O12 P3	1
MG	Magnesium ion	Mg	2

Water and common crystallization additives (NA) are not listed.

Primary citation

Crystal structure of the calcium pump with a bound ATP analogue in the absence of calcium. Toyoshima, C., Norimatsu, Y., Tsueda, J. To be published.

Other PDB entries of the same protein (UniProt P04191 (AlphaFold model), which also has an AlphaFold model), best resolution first:

27RD 2.0 Å, Crystal structure of SR Ca2+-ATPase in E2(TG) with bound IPP
27QZ 2.1 Å, Crystal structure of SR Ca2+-ATPase in E2(TG) with bound B1HQ
27RC 2.1 Å, Crystal structure of SR Ca2+-ATPase in E2(TG) with bound BMP
27QY 2.12 Å, Crystal structure of SR Ca2+-ATPase in E2(TG) with bound AHQ
3AR4 2.15 Å, Calcium pump crystal structure with bound ATP and TG in the absence of Ca2+
3AR7 2.15 Å, Calcium pump crystal structure with bound TNP-ATP and TG in the absence of Ca2+
27RE 2.2 Å, Crystal structure of SR Ca2+-ATPase in E2(TG) with bound MPQ
27RF 2.2 Å, Crystal structure of SR Ca2+-ATPase in E2(TG) with bound PHQ
3AR5 2.2 Å, Calcium pump crystal structure with bound TNP-AMP and TG
3AR6 2.2 Å, Calcium pump crystal structure with bound TNP-ADP and TG in the absence of calcium
3N5K 2.2 Å, Structure Of The (Sr)Ca2+-ATPase E2-AlF4- Form
1WPG 2.3 Å, Crystal structure of the SR CA2+-ATPase with MGF4

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