1vfp

Crystal structure of the SR CA2+-ATPase with bound AMPPCP

Method: X-RAY DIFFRACTION

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

Sarcoplasmic/endoplasmic reticulum calcium ATPase 1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 4 MAGNESIUM ION × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AT2A1_RABIT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–994； UniProt 1–994 Author chain B； PDBConstruct 1–994； UniProt 1–994

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	1vfp
Deposition date deposition_date	2004-04-18
Structure title title	Crystal structure of the SR CA2+-ATPase with bound AMPPCP
Keywords keywords	Membrane protein, P-type ATPase, HAD fold, HYDROLASE; HYDROLASE
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.

1vfp__assembly_1__model_1

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

Download this curve (.dat)

1vfp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vfp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	52.77 Å
Rg (electron density)	52.63 Å
Total Rg	52.63 Å
Atom count	15410
Residues	1988
Excluded volume	276790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vfp__assembly_1__model_1`	dimeric （2）	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 (5)

Entity 1 Entity 1 polymer

Description description	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Molecular weight formula_weight	109602.6 kDa
EC 编号 ec_number	3.6.3.8
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	15418

MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLWELVIEQFEDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEALKEYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMAATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAVALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQMSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLMKKEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGMLDPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIAMGSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAIGGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMALSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKLKALDLTQWLMVLKISLPVIGLDEILKFIARNYLEG

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
Molecular weight formula_weight	505.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1vfpa1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.7 — Metal cation-transporting ATPase, actuator domain A
Family Family family	b.82.7.1 — Metal cation-transporting ATPase, actuator domain A

Domain ID domain_id	d1vfpa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.7 — Meta-cation ATPase, catalytic domain P

Domain ID domain_id	d1vfpa3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.220 — Metal cation-transporting ATPase, ATP-binding domain N
Superfamily Superfamily superfamily	d.220.1 — Metal cation-transporting ATPase, ATP-binding domain N
Family Family family	d.220.1.1 — Metal cation-transporting ATPase, ATP-binding domain N

Domain ID domain_id	d1vfpa4
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.33 — Metal cation-transporting ATPase, transmembrane domain
Superfamily Superfamily superfamily	f.33.1 — Metal cation-transporting ATPase, transmembrane domain
Family Family family	f.33.1.1 — Metal cation-transporting ATPase, transmembrane domain

Domain ID domain_id	d1vfpb1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.7 — Metal cation-transporting ATPase, actuator domain A
Family Family family	b.82.7.1 — Metal cation-transporting ATPase, actuator domain A

Domain ID domain_id	d1vfpb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.7 — Meta-cation ATPase, catalytic domain P

Domain ID domain_id	d1vfpb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.220 — Metal cation-transporting ATPase, ATP-binding domain N
Superfamily Superfamily superfamily	d.220.1 — Metal cation-transporting ATPase, ATP-binding domain N
Family Family family	d.220.1.1 — Metal cation-transporting ATPase, ATP-binding domain N

Domain ID domain_id	d1vfpb4
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.33 — Metal cation-transporting ATPase, transmembrane domain
Superfamily Superfamily superfamily	f.33.1 — Metal cation-transporting ATPase, transmembrane domain
Family Family family	f.33.1.1 — Metal cation-transporting ATPase, transmembrane domain

CATH v4.4 (8 domains)

Domain ID domain_id	1vfpA01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	150 — Calcium-transporting ATPase, cytoplasmic transduction domain A
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic transduction domain A

Domain ID domain_id	1vfpA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1110 — Calcium-transporting ATPase, transmembrane domain
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, transmembrane domain

Domain ID domain_id	1vfpA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1110 — Calcium-transporting ATPase, cytoplasmic domain N
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic domain N

Domain ID domain_id	1vfpA04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	1vfpB01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	150 — Calcium-transporting ATPase, cytoplasmic transduction domain A
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic transduction domain A

Domain ID domain_id	1vfpB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1110 — Calcium-transporting ATPase, transmembrane domain
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, transmembrane domain

Domain ID domain_id	1vfpB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1110 — Calcium-transporting ATPase, cytoplasmic domain N
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic domain N

Domain ID domain_id	1vfpB04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

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Unit-cell length a length_a	90.920 Å
Unit-cell length b length_b	123.620 Å
Unit-cell length c length_c	151.820 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.21 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2550
R_work r_work	0.2470
R_free r_free	0.2870

Crystal structure of the SR CA2+-ATPase with bound AMPPCP

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

Sarcoplasmic/endoplasmic reticulum calcium ATPase 1

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

1vfp__assembly_1__model_1

1vfp__assembly_1__model_1 | I(q)

1vfp__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (4)

Crystal structure of the SR CA2+-ATPase with bound AMPPCP

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

Sarcoplasmic/endoplasmic reticulum calcium ATPase 1

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

1vfp__assembly_1__model_1

1vfp__assembly_1__model_1 | I(q)

1vfp__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (4)