2ZBD: PDB entry 2ZBD

Crystal Structure of the SR Calcium Pump with Bound Aluminium Fluoride, ADP and Calcium. Determined by X-ray diffraction at 2.4 Å resolution. Released 20 Nov 2007.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Oryctolagus cuniculus
Chains: 1
Atoms: 7,916
Mol. weight: 111.87 kDa
Ligands: PC1, ADP, ALF, MG
Released: 20 Nov 2007

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

Secondary structure: helices and β-sheets

2ZBD 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	42-44	3
α-helix	50-55	6
α-helix	60-74	15
α-helix	81-83	3
α-helix	84-120	37
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
α-helix	157	1
β-strand	158	1	3
α-helix	159	1
β-strand	162-168	7	2
β-strand	174-176	3	3
α-helix	178-181	4
β-strand	187-188	2	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	248-272	25
α-helix	276-278	3
α-helix	290-306	17
α-helix	310-328	19
β-strand	331-333	3	4
α-helix	338-344	7
β-strand	347-350	4	4
α-helix	352-356	5
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	424-428	5	7
β-strand	433-437	5	7
α-helix	440-451	12
α-helix	464-467	4
α-helix	470-476	7
β-strand	479-488	10	6
β-strand	493-500	8	6
α-helix	505-507	3
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	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	620-624	5	4
α-helix	629-638	10
β-strand	652-654	3	4
α-helix	655-659	5
α-helix	663-672	10
β-strand	675-677	3	4
α-helix	681-692	12
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	741-781	41
α-helix	783-785	3
α-helix	789-799	11
α-helix	802-805	4
α-helix	806-809	4
α-helix	810-813	4
α-helix	820-823	4
α-helix	831-856	26
α-helix	890-892	3
α-helix	894-914	21
α-helix	927-929	3
α-helix	931-949	19
α-helix	953-956	4
α-helix	961-963	3
α-helix	966-974	9
α-helix	976-986	11
α-helix	987-992	6

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

>2ZBD_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
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
ALF	Tetrafluoroaluminate ion	Al F4	1
MG	Magnesium ion	Mg	2
CA	Calcium ion	Ca	2

Primary citation

Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues. Toyoshima, C., Nomura, H., Tsuda, T. Nature (2004) 432:361-368. DOI 10.1038/nature02981 · PubMed

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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