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(-) Description

Title :  CRYSTAL STRUCTURE OF RECOMBINANT HUMAN HEXOKINASE TYPE I WITH 2-DEOXY-GLUCOSE 6-PHOSPHATE
 
Authors :  L. Shen, R. B. Honzatko
Date :  19 May 12  (Deposition) - 12 Jun 13  (Release) - 12 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hexokinase, 2-Deoxy Glucose-6-Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Shen, Y. Gao, R. B. Honzatko
Inhibitor Sites Of Unequal Affinity Linked By Binding Synergism In Mutant Forms Of Recombinant Human Hexokinase Type-I
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HEXOKINASE-1
    Chains: A, B
    EC Number: 2.7.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HK1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BRAIN FORM HEXOKINASE, HEXOKINASE TYPE I, HK I

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
10NZ4Ligand/Ion2-DEOXY-6-O-PHOSPHONO-BETA-D-ARABINO-HEXOPYRANOSE
2BGC4Ligand/IonBETA-D-GLUCOSE
3CIT1Ligand/IonCITRIC ACID
4NA4Ligand/IonSODIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
10NZ2Ligand/Ion2-DEOXY-6-O-PHOSPHONO-BETA-D-ARABINO-HEXOPYRANOSE
2BGC2Ligand/IonBETA-D-GLUCOSE
3CIT-1Ligand/IonCITRIC ACID
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
10NZ2Ligand/Ion2-DEOXY-6-O-PHOSPHONO-BETA-D-ARABINO-HEXOPYRANOSE
2BGC2Ligand/IonBETA-D-GLUCOSE
3CIT1Ligand/IonCITRIC ACID
4NA-1Ligand/IonSODIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:155 , PHE A:156 , PRO A:157 , THR A:172 , LYS A:173 , ASN A:208 , ASP A:209 , THR A:210 , ILE A:229 , ASN A:235 , GLU A:260 , GLN A:291 , GLU A:294 , HOH A:1198BINDING SITE FOR RESIDUE BGC A 1001
02AC2SOFTWAREASP A:84 , GLY A:87 , SER A:88 , ASP A:209 , GLY A:231 , THR A:232 , ASP A:413 , GLY A:414 , SER A:415 , SER A:449 , HOH A:1198BINDING SITE FOR RESIDUE 0NZ A 1002
03AC3SOFTWARESER A:603 , PHE A:604 , PRO A:605 , THR A:620 , LYS A:621 , ASN A:656 , ASP A:657 , THR A:658 , ILE A:677 , ASN A:683 , GLU A:708 , GLN A:739 , GLU A:742 , HOH A:1122BINDING SITE FOR RESIDUE BGC A 1003
04AC4SOFTWAREASP A:532 , GLY A:535 , THR A:536 , SER A:603 , ASP A:657 , GLY A:679 , THR A:680 , ASP A:861 , GLY A:862 , THR A:863 , SER A:897 , HOH A:1122 , HOH A:1184BINDING SITE FOR RESIDUE 0NZ A 1004
05AC5SOFTWARELEU A:242 , ILE A:245 , VAL A:248 , GLY A:250BINDING SITE FOR RESIDUE NA A 1005
06AC6SOFTWAREMET A:690 , VAL A:693 , VAL A:696 , GLY A:698BINDING SITE FOR RESIDUE NA A 1006
07AC7SOFTWARESER B:155 , PHE B:156 , PRO B:157 , THR B:172 , LYS B:173 , ASN B:208 , ASP B:209 , ILE B:229 , ASN B:235 , GLU B:260 , GLN B:291 , GLU B:294 , HOH B:1202BINDING SITE FOR RESIDUE BGC B 1001
08AC8SOFTWAREASP B:84 , SER B:88 , ASP B:209 , GLY B:231 , THR B:232 , ASP B:413 , GLY B:414 , SER B:415 , GLY B:448 , SER B:449 , HOH B:1139 , HOH B:1141 , HOH B:1196 , HOH B:1202BINDING SITE FOR RESIDUE 0NZ B 1002
09AC9SOFTWARESER B:603 , PHE B:604 , PRO B:605 , THR B:620 , LYS B:621 , ASN B:656 , ASP B:657 , THR B:658 , ILE B:677 , GLY B:681 , ASN B:683 , GLU B:708 , GLN B:739 , GLU B:742 , HOH B:1161BINDING SITE FOR RESIDUE BGC B 1003
10BC1SOFTWAREASP B:532 , GLY B:535 , THR B:536 , SER B:603 , ASP B:657 , GLY B:679 , THR B:680 , ASP B:861 , GLY B:862 , THR B:863 , GLY B:896 , SER B:897 , HOH B:1134 , HOH B:1161BINDING SITE FOR RESIDUE 0NZ B 1004
11BC2SOFTWARELEU B:242 , ILE B:245 , VAL B:248 , GLY B:250BINDING SITE FOR RESIDUE NA B 1005
12BC3SOFTWAREMET B:690 , VAL B:693 , VAL B:696 , GLY B:698BINDING SITE FOR RESIDUE NA B 1006
13BC4SOFTWAREPHE B:380 , GLN B:422 , ARG B:425 , ARG B:426BINDING SITE FOR RESIDUE CIT B 1007

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F9O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F9O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F9O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F9O)

(-) Exons   (0, 0)

(no "Exon" information available for 4F9O)

(-) 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:899
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4f9oa1 A:16-222 Mammalian type I hexokinase                                                                                                                                                                   d4f9oa2 A:223-465 Mammalian type I hexokinase                                                                                                                                                                                                      d4f9oa3 A:466-670 Mammalian type I hexokinase                                                                                                                                                                d4f9oa4 A:671-914 Mammalian type I hexokinase                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...........ee............eeeeeeee....eee..eeee....eeeee..eee..hhhhhh.hhhhhhhhhhhhhhhhhh.........eeeeee...ee.......ee...............hhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh..eeeeeee...eeeeeeee.hhh........eeeee.hhhhh..........hhhhhhhhhh........hhhhh...hhhhhhhhhhhhhhhh..hhhhh.hhhhhh....hhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeehhhhhhh.hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...........ee............eeeeeeee....eeeeeeeee.....eeeeeeeee..hhhhhh.hhhhhhhhhhhhhhhhhhhh......eeeeeee...eeeee..eeee...............hhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh....eeeeeee...eeeeeeee.hhh........eeeee.hhhhh..........hhhhhhhhhh........hhhhh...hhhhhhhhhhhhhhhh..hhhhh..hhhhh....hhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeehhhhhhh.hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f9o A  16 DDQVKKIDKYLYAMRLSDETLIDIMTRFRKEMKNGLSRDFNPTATVKMLPTFVRSIPDGSEKGDFIALDLGGSSFRILRVQVNHEKNQNVHMESEVYDTPENIVHGSGSQLFDHVAECLGDFMEKRKIKDKKLPVGFTFSFPCQQSKIDEAILITWTKRFKASGVEGADVVKLLNKAIKKRGDYDANIVAVVNDTVGTMMTCGYDDQHCEVGLIIGTGTNACYMEELRHIDLVEGDEGRMCINTEWGAFGDDGSLEDIRTEFDREIDRGSLNPGKQLFEKMVSGMYLGELVRLILVKMAKEGLLFEGRITPELLTRGKFNTSDVSAIEKNKEGLHNAKEILTRLGVEPSDDDCVSVQHVCTIVSFRSANLVAATLGAILNRLRDNKGTPRLRTTVGVDGSLYKTHPQYSRRFHKTLRRLVPDSDVRFLLSESGSGKGAAMVTAVAYRLAEQHRQIEETLAHFHLTKDMLLEVKKRMRAEMELGLRKQTHNNAVVKMLPSFVRRTPDGTENGDFLALDLGGTNFRVLLVKIRSGKKRTVEMHNKIYAIPIEIMQGTGEELFDHIVSCISDFLDYMGIKGPRMPLGFTFSFPCQQTSLDAGILITWTKGFKATDCVGHDVVTLLRDAIKRREEFDLDVVAVVNDTVGTMMTCAYEEPTCEVGLIVGTGSNACYMEEMKNVEMVEGDQGQMCINMEWGAFGDNGCLDDIRTHYDRLVDEYSLNAGKQRYEKMISGMYLGEIVRNILIDFTKKGFLFRGQISETLKTRGIFETKFLSQIESDRLALLQVRAILQQLGLNSTCDDSILVKTVCGVVSRRAAQLCGAGMAAVVDKIRENRGLDRLNVTVGVDGTLYKLHPHFSRIMHQTVKELSPKCNVSFLLSEDGSGKGAALITAVGVRLRTE 914
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905         


Chain B from PDB  Type:PROTEIN  Length:899
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4f9ob1 B:16-222 Mammalian type I hexokinase                                                                                                                                                                   d4f9ob2 B:223-465 Mammalian type I hexokinase                                                                                                                                                                                                      d4f9ob3 B:466-670 Mammalian type I hexokinase                                                                                                                                                                d4f9ob4 B:671-914 Mammalian type I hexokinase                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhh....ee............eeeeeeee....eeeeeeee.......eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee...ee.......ee...............hhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh..eeeeeee...eeeeeeee............eeeee.hhhhh..........hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhh....hhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeehhhhhhh.hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh......ee............eeeeeeee....eeeeeeeee.....eeeeeeeee..hhhhhh.hhhhhhhhhhhhhhhhhhhh.......eeeeee...eeeee..eeee...............hhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhh....eeeeeee...eeeeeeee............eeeee.hhhhh..........hhhhhhhhhh........hhhhh...hhhhhhhhhhhhhhhh..hhhhh.hhhhhh....hhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeehhhhhhh.hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f9o B  16 DDQVKKIDKYLYAMRLSDETLIDIMTRFRKEMKNGLSRDFNPTATVKMLPTFVRSIPDGSEKGDFIALDLGGSSFRILRVQVNHEKNQNVHMESEVYDTPENIVHGSGSQLFDHVAECLGDFMEKRKIKDKKLPVGFTFSFPCQQSKIDEAILITWTKRFKASGVEGADVVKLLNKAIKKRGDYDANIVAVVNDTVGTMMTCGYDDQHCEVGLIIGTGTNACYMEELRHIDLVEGDEGRMCINTEWGAFGDDGSLEDIRTEFDREIDRGSLNPGKQLFEKMVSGMYLGELVRLILVKMAKEGLLFEGRITPELLTRGKFNTSDVSAIEKNKEGLHNAKEILTRLGVEPSDDDCVSVQHVCTIVSFRSANLVAATLGAILNRLRDNKGTPRLRTTVGVDGSLYKTHPQYSRRFHKTLRRLVPDSDVRFLLSESGSGKGAAMVTAVAYRLAEQHRQIEETLAHFHLTKDMLLEVKKRMRAEMELGLRKQTHNNAVVKMLPSFVRRTPDGTENGDFLALDLGGTNFRVLLVKIRSGKKRTVEMHNKIYAIPIEIMQGTGEELFDHIVSCISDFLDYMGIKGPRMPLGFTFSFPCQQTSLDAGILITWTKGFKATDCVGHDVVTLLRDAIKRREEFDLDVVAVVNDTVGTMMTCAYEEPTCEVGLIVGTGSNACYMEEMKNVEMVEGDQGQMCINMEWGAFGDNGCLDDIRTHYDRLVDEYSLNAGKQRYEKMISGMYLGEIVRNILIDFTKKGFLFRGQISETLKTRGIFETKFLSQIESDRLALLQVRAILQQLGLNSTCDDSILVKTVCGVVSRRAAQLCGAGMAAVVDKIRENRGLDRLNVTVGVDGTLYKLHPHFSRIMHQTVKELSPKCNVSFLLSEDGSGKGAALITAVGVRLRTE 914
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F9O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F9O)

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)

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        HXK1_HUMAN | P19367: 1cza 1dgk 1hkb 1hkc 1qha 4foe 4foi 4fpa 4fpb

(-) Related Entries Specified in the PDB File

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