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- PDB-2aw0: FOURTH METAL-BINDING DOMAIN OF THE MENKES COPPER-TRANSPORTING ATP... -

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Basic information

Entry
Database: PDB / ID: 2aw0
TitleFOURTH METAL-BINDING DOMAIN OF THE MENKES COPPER-TRANSPORTING ATPASE, NMR, 20 STRUCTURES
ComponentsMENKES COPPER-TRANSPORTING ATPASE
KeywordsCOPPER TRANSPORT / COPPER-TRANSPORTING ATPASE / COPPER-BINDING DOMAIN / HYDROLASE
Function / homology
Function and homology information


peptidyl-lysine modification / epinephrine metabolic process / : / positive regulation of response to wounding / cellular response to cobalt ion / L-tryptophan metabolic process / Ion influx/efflux at host-pathogen interface / positive regulation of tyrosinase activity / copper-dependent protein binding / cerebellar Purkinje cell differentiation ...peptidyl-lysine modification / epinephrine metabolic process / : / positive regulation of response to wounding / cellular response to cobalt ion / L-tryptophan metabolic process / Ion influx/efflux at host-pathogen interface / positive regulation of tyrosinase activity / copper-dependent protein binding / cerebellar Purkinje cell differentiation / elastic fiber assembly / response to iron(III) ion / P-type divalent copper transporter activity / copper ion export / copper ion import / copper ion transmembrane transporter activity / P-type Cu+ transporter / P-type monovalent copper transporter activity / positive regulation of melanin biosynthetic process / cellular response to lead ion / superoxide dismutase copper chaperone activity / regulation of oxidative phosphorylation / positive regulation of catalytic activity / catecholamine metabolic process / copper ion transport / pyramidal neuron development / serotonin metabolic process / trans-Golgi network transport vesicle / melanosome membrane / detoxification of copper ion / norepinephrine metabolic process / T-helper cell differentiation / positive regulation of vascular associated smooth muscle cell migration / collagen fibril organization / negative regulation of iron ion transmembrane transport / response to manganese ion / cartilage development / cellular response to antibiotic / hair follicle morphogenesis / pigmentation / response to zinc ion / skin development / lung alveolus development / cellular response to cadmium ion / Detoxification of Reactive Oxygen Species / blood vessel development / cell leading edge / dopamine metabolic process / central nervous system neuron development / cuprous ion binding / Ion transport by P-type ATPases / microvillus / blood vessel remodeling / intracellular copper ion homeostasis / positive regulation of cell size / positive regulation of lamellipodium assembly / cellular response to copper ion / cellular response to platelet-derived growth factor stimulus / lactation / extracellular matrix organization / removal of superoxide radicals / neuron projection morphogenesis / secretory granule / liver development / positive regulation of epithelial cell proliferation / trans-Golgi network membrane / cellular response to iron ion / female pregnancy / mitochondrion organization / locomotory behavior / cellular response to amino acid stimulus / trans-Golgi network / brush border membrane / small GTPase binding / phagocytic vesicle membrane / late endosome / protein-folding chaperone binding / early endosome membrane / basolateral plasma membrane / cellular response to hypoxia / perikaryon / in utero embryonic development / neuron projection / postsynaptic density / apical plasma membrane / copper ion binding / axon / neuronal cell body / dendrite / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / E1-E2 ATPase ...Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SILVER ION / Copper-transporting ATPase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsGitschier, J. / Fairbrother, W.J.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Solution structure of the fourth metal-binding domain from the Menkes copper-transporting ATPase.
Authors: Gitschier, J. / Moffat, B. / Reilly, D. / Wood, W.I. / Fairbrother, W.J.
History
DepositionOct 8, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MENKES COPPER-TRANSPORTING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7442
Polymers7,6371
Non-polymers1081
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40LOWEST RESIDUAL RESTRAINT VIOLATION ENERGIES
Representative

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Components

#1: Protein MENKES COPPER-TRANSPORTING ATPASE


Mass: 7636.557 Da / Num. of mol.: 1 / Fragment: FOURTH METAL-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: AG(I)-BOUND STATE / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q04656, EC: 3.6.1.36
#2: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ag

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112QF COSY
121TOCSY (30 AND 70 MS)
131NOESY(100 AND 200 MS)
141ROESY(40 MS)
151COSY-35

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Sample preparation

Sample conditionspH: 6.8 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
DiscoverMSIrefinement
DGIIstructure solution
Discoverstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST RESIDUAL RESTRAINT VIOLATION ENERGIES
Conformers calculated total number: 40 / Conformers submitted total number: 20

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