Author Archives: Stephen Gallik

Peptide Synthetase

PDB ID:   2VSQ

Number of Polypeptide Chains in the Protein:   1

Chain Designation:  

Chain 1: A

Gene Names:  

srfAC, srfA3, BSU03510

PDB Deposition Title:  

STRUCTURE OF SURFACTIN A SYNTHETASE C (SRFA-C), A NONRIBOSOMAL PEPTIDE SYNTHETASE TERMINATION MODULE

Primary Citation Title:  

Crystal structure of the termination module of a nonribosomal peptide synthetase.

Citation Authors:  

Tanovic, A., Samel, S.A., Essen, L.-O., Marahiel, M.A.

Citation Journal:  

Journal: (2008) Science 321: 659

Related PDB Entries:  

1JMK,

 


Information for Chain A;  UniprotKB Accession Number:  Q08787

Primary Structure

Length of the Chain (from Uniprot Q08787):  1275

FASTA Sequence for the chain (from Uniprot Q08787):

>sp|Q08787|SRFAC_BACSU Surfactin synthase subunit 3 OS=Bacillus subtilis (strain 168) GN=srfAC PE=1 SV=2
MSQFSKDQVQDMYYLSPMQEGMLFHAILNPGQSFYLEQITMKVKGSLNIKCLEESMNVIM
DRYDVFRTVFIHEKVKRPVQVVLKKRQFHIEEIDLTHLTGSEQTAKINEYKEQDKIRGFD
LTRDIPMRAAIFKKAEESFEWVWSYHHIILDGWCFGIVVQDLFKVYNALREQKPYSLPPV
KPYKDYIKWLEKQDKQASLRYWREYLEGFEGQTTFAEQRKKQKDGYEPKELLFSLSEAET
KAFTELAKSQHTTLSTALQAVWSVLISRYQQSGDLAFGTVVSGRPAEIKGVEHMVGLFIN
VVPRRVKLSEGITFNGLLKRLQEQSLQSEPHQYVPLYDIQSQADQPKLIDHIIVFENYPL
QDAKNEESSENGFDMVDVHVFEKSNYDLNLMASPGDEMLIKLAYNENVFDEAFILRLKSQ
LLTAIQQLIQNPDQPVSTINLVDDREREFLLTGLNPPAQAHETKPLTYWFKEAVNANPDA
PALTYSGQTLSYRELDEEANRIARRLQKHGAGKGSVVALYTKRSLELVIGILGVLKAGAA
YLPVDPKLPEDRISYMLADSAAACLLTHQEMKEQAAELPYTGTTLFIDDQTRFEEQASDP
ATAIDPNDPAYIMYTSGTTGKPKGNITTHANIQGLVKHVDYMAFSDQDTFLSVSNYAFDA
FTFDFYASMLNAARLIIADEHTLLDTERLTDLILQENVNVMFATTALFNLLTDAGEDWMK
GLRCILFGGERASVPHVRKALRIMGPGKLINCYGPTEGTVFATAHVVHDLPDSISSLPIG
KPISNASVYILNEQSQLQPFGAVGELCISGMGVSKGYVNRADLTKEKFIENPFKPGETLY
RTGDLARWLPDGTIEYAGRIDDQVKIRGHRIELEEIEKQLQEYPGVKDAVVVADRHESGD
ASINAYLVNRTQLSAEDVKAHLKKQLPAYMVPQTFTFLDELPLTTNGKVNKRLLPKPDQD
QLAEEWIGPRNEMEETIAQIWSEVLGRKQIGIHDDFFALGGHSLKAMTAASRIKKELGID
LPVKLLFEAPTIAGISAYLKNGGSDGLQDVTIMNQDQEQIIFAFPPVLGYGLMYQNLSSR
LPSYKLCAFDFIEEEDRLDRYADLIQKLQPEGPLTLFGYSAGCSLAFEAAKKLEEQGRIV
QRIIMVDSYKKQGVSDLDGRTVESDVEALMNVNRDNEALNSEAVKHGLKQKTHAFYSYYV
NLISTGQVKADIDLLTSGADFDMPEWLASWEEATTGVYRVKRGFGTHAEMLQGETLDRNA
EILLEFLNTQTVTVS

Secondary Structures (DSSP defined; from RCSB PDB)

Helical Structures:  Number of Helices:  ;  Percentage of Residues:  

Beta Strands:  Number of Strands:  ;  Percentage of Residues:  

Secondary Structure Map:

 

Tertiary Structure

Number of Domains Along Chain A:  

CATH Domain IDs:  

CATH Classes:  

CATH Architectures:  

CATH Topologies:  

Topological Diagrams:

 

 

Function and Ligand Binding Site

Excerpt from Abstract:

Description of Function from Uniprot:

Selected Molecular Function GO Terms:

EC Number:   

EC Description:   

Major Organic Ligand:   

Ligand Binding Residues:

Ligand Binding Site:

Hexokinase

PDB ID:   1BDG

Number of Polypeptide Chains in the Protein:   1

Chain Designation:  

Chain 1: A

Gene Names:  

N/A

PDB Deposition Title:  

HEXOKINASE FROM SCHISTOSOMA MANSONI COMPLEXED WITH GLUCOSE

Primary Citation Title:  

The structure of mammalian hexokinase-1.

Citation Authors:  

Mulichak, A.M., Wilson, J.E., Padmanabhan, K., Garavito, R.M.

Citation Journal:  

Journal: (1998) Nat.Struct.Biol. 5: 555-560

Related PDB Entries:  

1BDG, 1BG3

 


Information for Chain A;  UniprotKB Accession Number:  Q26609

Primary Structure

Length of the Chain (from Uniprot Q26609):  451

FASTA Sequence for the chain (from Uniprot Q26609):

>sp|Q26609|HXK_SCHMA Hexokinase OS=Schistosoma mansoni PE=1 SV=2
MVFSDQQLFEKVVEILKPFDLSVVDYEEICDRMGESMRLGLQKSTNEKSSIKMFPSYVTK
TPNGTETGNFLALDLGGTNYRVLSVTLEGKGKSPRIQERTYCIPAEKMSGSGTELFKYIA
ETLADFLENNGMKDKKFDLGFTFSFPCVQKGLTHATLVRWTKGFSADGVEGHNVAELLQT
ELDKRELNVKCVAVVNDTVGTLASCALEDPKCAVGLIVGTGTNVAYIEDSSKVELMDGVK
EPEVVINTEWGAFGEKGELDCWRTQFDKSMDIDSLHPGKQLYEKMVSGMYLGELVRHIIV
YLVEQKILFRGDLPERLKVRNSLLTRYLTDVERDPAHLLYNTHYMLTDDLHVPVVEPIDN
RIVRYACEMVVKRAAYLAGAGIACILRRINRSEVTVGVDGSLYKFHPKFCERMTDMVDKL
KPKNTRFCLRLSEDGSGKGAAAIAASCTRQN

Secondary Structures (DSSP defined; from RCSB PDB)

Helical Structures:  Number of Helices:  20;  Percentage of Residues:  42

Beta Strands:  Number of Strands:  16;  Percentage of Residues:  18

Secondary Structure Map:

 

Tertiary Structure

Number of Domains Along Chain A:  2

CATH Domain IDs:  1bdgA01, 1bdgA02

CATH Classes:  A01: Alpha Beta, A02: Alpha Beta

CATH Architectures:  A01: 3-layer (aba) Sandwich, A02: 2-layer Sandwich

CATH Topologies:  A01: Hexokinase; domain 1, A02: Nucleotidyltransferase

Topological Diagrams:
,

 

 

Function and Ligand Binding Site

Excerpt from Abstract:

Not applicable.

Description of Function from Uniprot:

ATP + D-hexose = ADP + D-hexose 6-phosphate.

Selected Molecular Function GO Terms:

GO ID: 0005524, Name: ATP Binding, Definition: Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

  ||  

Go ID: 0004396, Name: Hexokinase Activity, Definition: Catalysis of the reaction: ATP + D-hexose = ADP + D-hexose 6-phosphate.

EC Number:   EC 2.7.1.1

EC Description:   

A transferase that transfers phosphorus-containing groups. Phosphotransferases with an alcohol group as acceptor.

Major Organic Ligand:   ALPHA-D-GLUCOSE

Ligand Binding Residues:

Ser 155, Phe 156, Pro 157, Thr 172, Lys 173, Asn 208, Asp 209, Ile 229, Gly 233, Thr 234, Asn 235, Glu 260, Glu 294

Ligand Binding Site:

Sodium/potassium-transporting ATPase

PDB ID:   3B8E

Number of Polypeptide Chains in the Protein:   6

Chain Designation:  

Chain 1: A, C; Chain2: B, D; Chain 3: G, H

Gene Names:  

ATP1A1, ATP1B1, FXYD2

PDB Deposition Title:  

Crystal structure of the sodium-potassium pump

Primary Citation Title:  

Crystal structure of the sodium-potassium pump.

Citation Authors:  

Morth, J.P., Pedersen, B.P., Toustrup-Jensen, M.S., Sorensen, T.L., Petersen, J., Andersen, J.P., Vilsen, B., Nissen, P.

Citation Journal:  

(2007) Nature 450: 1043-1049

Related PDB Entries:  

3KDP, 3N23, 3N2F, 3WGU, 3WGV

 


Information for Chain A;  UniprotKB Accession Number:  P05024

Primary Structure

Length of the Chain (from Uniprot P05024):  1021

FASTA Sequence for the chain (from Uniprot P05024):

>sp|P05024|AT1A1_PIG Sodium/potassium-transporting ATPase subunit alpha-1 OS=Sus scrofa GN=ATP1A1 PE=1 SV=1
MGKGVGRDKYEPAAVSEHGDKKKAKKERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRG
LTPARAAEILARDGPNALTPPPTTPEWVKFCRQLFGGFSMLLWIGAILCFLAYGIQAATE
EEPQNDNLYLGVVLSAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIRNGEKMSINA
EEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNI
AFFSTNCVEGTARGIVVYTGDRTVMGRIATLASGLEGGQTPIAAEIEHFIHIITGVAVFL
GVSFFILSLILEYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLE
AVETLGSTSTICSDKTGTLTQNRMTVAHMWSDNQIHEADTTENQSGVSFDKTSATWLALS
RIAGLCNRAVFQANQENLPILKRAVAGDASESALLKCIELCCGSVKEMRERYTKIVEIPF
NSTNKYQLSIHKNPNTAEPRHLLVMKGAPERILDRCSSILIHGKEQPLDEELKDAFQNAY
LELGGLGERVLGFCHLFLPDEQFPEGFQFDTDDVNFPLDNLCFVGLISMIDPPRAAVPDA
VGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKA
CVVHGSDLKDMTSEQLDDILKYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDS
PASKKADIGVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTS
NIPEITPFLIFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTD
KLVNEQLISMAYGQIGMIQALGGFFTYFVILAENGFLPIHLLGLRVNWDDRWINDVEDSY
GQQWTYEQRKIVEFTCHTPFFVTIVVVQWADLVICKTRRNSVFQQGMKNKILIFGLFEET
ALAAFLSYCPGMGVALRMYPLKPTWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKETY
Y

Secondary Structures (DSSP defined; from RCSB PDB)

Helical Structures:  Number of Helices:  ;  Percentage of Residues:  

Beta Strands:  Number of Strands:  ;  Percentage of Residues:  

Secondary Structure Map:

 

Tertiary Structure

Number of Domains Along Chain A:  

CATH Domain IDs:  

CATH Classes:  

CATH Architectures:  

CATH Topologies:  

Topological Diagrams:

 

 

Function and Ligand Binding Site

Excerpt from Abstract:

Description of Function from Uniprot:

Selected Molecular Function GO Terms:

EC Number:   

EC Description:   

Major Organic Ligand:   

Ligand Binding Residues:

Ligand Binding Site:

Myoglobin

PDB ID:   1MBN

Number of Polypeptide Chains in the Protein:   1

Chain Designation:  

Chain 1: A

Gene Names:  

MB

PDB Deposition Title:  

The stereochemistry of the protein myoglobin

Primary Citation Title:  

The Stereochemistry of the Protein Myoglobin

Citation Authors:  

Watson, H.C.

Citation Journal:  

(1969) Prog.Stereochem. 4: 299

Related PDB Entries:  

1A6G, 1ABS, 1BVC, 1MBD

 


Information for Chain A;  UniprotKB Accession Number:  P02185

Primary Structure

Length of the Chain (from Uniprot P02185):  154

FASTA Sequence for the chain (from Uniprot P02185):

>sp|P02185|MYG_PHYCD Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2
MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASE
DLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRH
PGDFGADAQGAMNKALELFRKDIAAKYKELGYQG

Secondary Structures (DSSP defined; from RCSB PDB)

Helical Structures:  Number of Helices:  9;  Percentage of Residues:  77

Beta Strands:  Number of Strands:  0;  Percentage of Residues:  0

Secondary Structure Map:

 

Tertiary Structure

Number of Domains Along Chain A:  1

CATH Domain IDs:  1mbnA00

CATH Classes:  A00: Mainly Alpha

CATH Architectures:  A00: Orthogonal Bundle

CATH Topologies:  A00: Globin-like

Topological Diagrams:

 

 

Function and Ligand Binding Site

Excerpt from Abstract:

The PubMed Abstract is not available.

Description of Function from Uniprot:

Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.

Selected Molecular Function GO Terms:

GO ID: 0020037; Name: Heme Binding; Description: Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.

  ||  

GO ID: 0020037; Name: Heme Binding; Description: Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.

EC Number:   3.12.12.11

EC Description:   

Oxygen binding & Transport Protein

Major Organic Ligand:   

Ligand Binding Residues:

Phe 43, Arg 45, His 64, Ala 71, Leu 89, Ser 92, His 93, His 97, Ile 99, Tyr 103, Ile 107, Phe 138

Ligand Binding Site: