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(-) Description

Title :  STRUCTURE OF K57A HPNMT WITH INHIBITOR 3-HYDROXYMETHYL-7-(N-4-CHLOROPHENYLAMINOSULFONYL)-THIQ AND ADOHCY (SAH)
 
Authors :  N. Drinkwater, J. L. Martin
Date :  19 Dec 06  (Deposition) - 09 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. L. Gee, N. Drinkwater, J. D. A. Tyndall, G. L. Grunewald, Q. Wu, M. J. Mcleish, J. L. Martin
Enzyme Adaptation To Inhibitor Binding: A Cryptic Binding Site In Phenylethanolamine N-Methyltransferase
J. Med. Chem. V. 50 4845 2007
PubMed-ID: 17845018  |  Reference-DOI: 10.1021/JM0703385

(-) Compounds

Molecule 1 - PHENYLETHANOLAMINE N-METHYLTRANSFERASE
    ChainsA, B
    EC Number2.1.1.28
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNMT-HIS
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPNMTASE, NORADRENALINE N-METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1F832Ligand/Ion(3R)-N-(4-CHLOROPHENYL)-3-(HYDROXYMETHYL)-1,2,3,4-TETRAHYDROISOQUINOLINE-7-SULFONAMIDE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1F831Ligand/Ion(3R)-N-(4-CHLOROPHENYL)-3-(HYDROXYMETHYL)-1,2,3,4-TETRAHYDROISOQUINOLINE-7-SULFONAMIDE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1F831Ligand/Ion(3R)-N-(4-CHLOROPHENYL)-3-(HYDROXYMETHYL)-1,2,3,4-TETRAHYDROISOQUINOLINE-7-SULFONAMIDE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1F832Ligand/Ion(3R)-N-(4-CHLOROPHENYL)-3-(HYDROXYMETHYL)-1,2,3,4-TETRAHYDROISOQUINOLINE-7-SULFONAMIDE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:35 , ASN A:39 , TYR A:40 , ARG A:44 , VAL A:53 , GLY A:54 , LEU A:58 , TYR A:85 , TYR A:126 , PHE A:182 , GLU A:219 , TYR A:222 , MET A:258 , ASP A:267 , HOH A:3026 , HOH A:3085BINDING SITE FOR RESIDUE F83 A 2001
2AC2SOFTWARETYR B:535 , ASN B:539 , TYR B:540 , ARG B:544 , VAL B:553 , GLY B:554 , LEU B:558 , TYR B:585 , PHE B:682 , ALA B:686 , GLU B:719 , TYR B:722 , MET B:758 , ASP B:767 , HOH B:3038 , HOH B:3120BINDING SITE FOR RESIDUE F83 B 2002
3AC3SOFTWARETYR A:27 , TYR A:35 , TYR A:40 , GLY A:79 , SER A:80 , GLY A:81 , THR A:83 , TYR A:85 , ASP A:101 , PHE A:102 , LEU A:103 , ASN A:106 , ASP A:158 , VAL A:159 , HIS A:160 , ALA A:181 , PHE A:182 , CYS A:183 , VAL A:187BINDING SITE FOR RESIDUE SAH A 3001
4AC4SOFTWARETYR B:527 , TYR B:535 , TYR B:540 , GLY B:579 , SER B:580 , GLY B:581 , THR B:583 , TYR B:585 , ASP B:601 , PHE B:602 , LEU B:603 , ASN B:606 , ILE B:657 , ASP B:658 , VAL B:659 , HIS B:660 , ALA B:681 , PHE B:682 , CYS B:683 , VAL B:687BINDING SITE FOR RESIDUE SAH B 3002

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:48 -B:639
2A:139 -B:548

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:42 -Pro A:43
2Leu A:173 -Pro A:174
3Pro B:542 -Pro B:543
4Leu B:673 -Pro B:674

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 16)

Asymmetric Unit (8, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036829T98APNMT_HUMANPolymorphism36060376A
B
T98
598
A
2UniProtVAR_036830R112CPNMT_HUMANPolymorphism34530498A
B
R112
612
C
3UniProtVAR_036831A175TPNMT_HUMANPolymorphism34341496A
B
A175
675
T
4UniProtVAR_037611S188CPNMT_HUMANPolymorphism5639A
B
S188
688
C
5UniProtVAR_037612L211HPNMT_HUMANPolymorphism5640A
B
L211
711
H
6UniProtVAR_037613L217QPNMT_HUMANPolymorphism5641A
B
L217
717
Q
7UniProtVAR_037614R254HPNMT_HUMANPolymorphism5642A
B
R254
754
H
8UniProtVAR_024547W276RPNMT_HUMANPolymorphism5643A
B
W276
776
R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036829T98APNMT_HUMANPolymorphism36060376A
A
T98
598
A
2UniProtVAR_036830R112CPNMT_HUMANPolymorphism34530498A
A
R112
612
C
3UniProtVAR_036831A175TPNMT_HUMANPolymorphism34341496A
A
A175
675
T
4UniProtVAR_037611S188CPNMT_HUMANPolymorphism5639A
A
S188
688
C
5UniProtVAR_037612L211HPNMT_HUMANPolymorphism5640A
A
L211
711
H
6UniProtVAR_037613L217QPNMT_HUMANPolymorphism5641A
A
L217
717
Q
7UniProtVAR_037614R254HPNMT_HUMANPolymorphism5642A
A
R254
754
H
8UniProtVAR_024547W276RPNMT_HUMANPolymorphism5643A
A
W276
776
R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036829T98APNMT_HUMANPolymorphism36060376A
B
T98
598
A
2UniProtVAR_036830R112CPNMT_HUMANPolymorphism34530498A
B
R112
612
C
3UniProtVAR_036831A175TPNMT_HUMANPolymorphism34341496A
B
A175
675
T
4UniProtVAR_037611S188CPNMT_HUMANPolymorphism5639A
B
S188
688
C
5UniProtVAR_037612L211HPNMT_HUMANPolymorphism5640A
B
L211
711
H
6UniProtVAR_037613L217QPNMT_HUMANPolymorphism5641A
B
L217
717
Q
7UniProtVAR_037614R254HPNMT_HUMANPolymorphism5642A
B
R254
754
H
8UniProtVAR_024547W276RPNMT_HUMANPolymorphism5643A
B
W276
776
R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (8, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036829T98APNMT_HUMANPolymorphism36060376A
A/B
T98
598
A
2UniProtVAR_036830R112CPNMT_HUMANPolymorphism34530498A
A/B
R112
612
C
3UniProtVAR_036831A175TPNMT_HUMANPolymorphism34341496A
A/B
A175
675
T
4UniProtVAR_037611S188CPNMT_HUMANPolymorphism5639A
A/B
S188
688
C
5UniProtVAR_037612L211HPNMT_HUMANPolymorphism5640A
A/B
L211
711
H
6UniProtVAR_037613L217QPNMT_HUMANPolymorphism5641A
A/B
L217
717
Q
7UniProtVAR_037614R254HPNMT_HUMANPolymorphism5642A
A/B
R254
754
H
8UniProtVAR_024547W276RPNMT_HUMANPolymorphism5643A
A/B
W276
776
R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 3)

Asymmetric Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_NNMT_PNMT_TEMTPS51681 SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.PNMT_HUMAN23-282  1B:523-782
2NNMT_PNMT_TEMTPS01100 NNMT/PNMT/TEMT family of methyltransferases signature.PNMT_HUMAN75-91
 
  2A:75-91
B:575-591
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_NNMT_PNMT_TEMTPS51681 SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.PNMT_HUMAN23-282  0-
2NNMT_PNMT_TEMTPS01100 NNMT/PNMT/TEMT family of methyltransferases signature.PNMT_HUMAN75-91
 
  1A:75-91
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_NNMT_PNMT_TEMTPS51681 SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.PNMT_HUMAN23-282  1B:523-782
2NNMT_PNMT_TEMTPS01100 NNMT/PNMT/TEMT family of methyltransferases signature.PNMT_HUMAN75-91
 
  1-
B:575-591
Biological Unit 3 (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_NNMT_PNMT_TEMTPS51681 SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.PNMT_HUMAN23-282  1B:523-782
2NNMT_PNMT_TEMTPS01100 NNMT/PNMT/TEMT family of methyltransferases signature.PNMT_HUMAN75-91
 
  2A:75-91
B:575-591

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000002695822ENSE00000950701chr17:37824507-37824930424PNMT_HUMAN1-68682A:24-68
B:514-568
45
55
1.3ENST000002695823ENSE00001682624chr17:37825882-37826089208PNMT_HUMAN68-137702A:68-137
B:568-637
70
70
1.4bENST000002695824bENSE00000950703chr17:37826204-37826728525PNMT_HUMAN137-2821462A:137-280
B:637-782
144
146

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:257
 aligned with PNMT_HUMAN | P11086 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:257
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       
           PNMT_HUMAN    24 ASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKV 280
               SCOP domains d2obfa_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2obfA00 A:24-280 Vaccinia Virus protein VP39                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.hhhhhhhhhh...........hhhhhhhhhhhhhhhh......eeeee.....hhhhh.hhhhh.eeeee..hhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhheeeee...................eeeeeee.hhhhh..hhhhhhhhhhhhhh.eeeeeeeeeeeee...eeee..eeee....hhhhhhhhhhhh.eeeeeeeeee.hhhhh.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) SAM_MT_NNMT_PNMT_TEMT  PDB: - UniProt: 23-282                                                                                                                                                                                                                     PROSITE (1)
                PROSITE (2) ---------------------------------------------------NNMT_PNMT_TEMT   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:24-68 UniProt: 1-68         --------------------------------------------------------------------Exon 1.4b  PDB: A:137-280 UniProt: 137-282 [INCOMPLETE]                                                                                          Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.3  PDB: A:68-137 UniProt: 68-137                               ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2obf A  24 ASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWALRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKV 280
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       

Chain B from PDB  Type:PROTEIN  Length:269
 aligned with PNMT_HUMAN | P11086 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:269
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273         
           PNMT_HUMAN    14 PDSAPGQAAVASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKVGL 282
               SCOP domains d2obfb_ B: automated matches                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2obfB00 B:514-782 Vaccinia Virus protein VP39                                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) NNMT_PNMT_TEMT-2obfB01 B:514-779                                                                                                                                                                                                                                          --- Pfam domains (1)
           Pfam domains (2) NNMT_PNMT_TEMT-2obfB02 B:514-779                                                                                                                                                                                                                                          --- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh......eeeee.....hhhhh.hhhhh.eeeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhheeeeee..................eeeeeee.hhhhhh.hhhhhhhhhhhhhh.eeeeeeeeeeeee...eeee..eeee....hhhhhhhhhhhh.eeeeeeeeee.hhhhh.......eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------A-------------C--------------------------------------------------------------T------------C----------------------H-----Q------------------------------------H---------------------R------ SAPs(SNPs)
                PROSITE (1) ---------SAM_MT_NNMT_PNMT_TEMT  PDB: B:523-782 UniProt: 23-282                                                                                                                                                                                                                PROSITE (1)
                PROSITE (2) -------------------------------------------------------------NNMT_PNMT_TEMT   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: B:514-568 UniProt: 1-68 [INCOMPLETE]    --------------------------------------------------------------------Exon 1.4b  PDB: B:637-782 UniProt: 137-282                                                                                                         Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.3  PDB: B:568-637 UniProt: 68-137                              ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2obf B 514 PDSAPGQAAVASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWALRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKVGL 782
                                   523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773         

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PNMT_HUMAN | P11086)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0004603    phenylethanolamine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + phenylethanolamine = S-adenosyl-L-homocysteine + N-methylphenylethanolamine.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0042423    catecholamine biosynthetic process    The chemical reactions and pathways resulting in the formation of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
    GO:0042418    epinephrine biosynthetic process    The chemical reactions and pathways resulting in the formation of epinephrine, a hormone produced by the medulla of the adrenal glands that increases heart activity, improves the power and prolongs the action of muscles, and increases the rate and depth of breathing. It is synthesized by the methylation of norepinephrine.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PNMT_HUMAN | P110861hnn 1n7i 1n7j 1yz3 2an3 2an4 2an5 2g70 2g71 2g72 2g8n 2ony 2onz 2opb 3hca 3hcb 3hcc 3hcd 3hce 3hcf 3kpj 3kpu 3kpv 3kpw 3kpy 3kqm 3kqo 3kqp 3kqq 3kqs 3kqt 3kqv 3kqw 3kqy 3kr0 3kr1 3kr2 4dm3 4mik 4mq4

(-) Related Entries Specified in the PDB File

1hnn CRYSTAL STRUCTURE OF HUMAN PNMT COMPLEXED WITH SK&F 29661 AND ADOHCY (SAH)
2g8n STRUCTURE OF HUMAN PNMT IN COMPLEX WITH INHIBITOR 3- HYDROXYMETHYL-7-NITRO-THIQ AND ADO-HCY (SAH)