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(-) Description

Title :  CRYSTAL STRUCTURE OF RECOMBINANT HUMAN HEXOKINASE TYPE I WITH MANNOSE 6-PHOSPHATE
 
Authors :  L. Shen, R. B. Honzatko
Date :  20 Jun 12  (Deposition) - 03 Jul 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hexokinase, Mannose 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/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
1BGC4Ligand/IonBETA-D-GLUCOSE
2CIT2Ligand/IonCITRIC ACID
3M6D4Ligand/Ion6-O-PHOSPHONO-BETA-D-MANNOPYRANOSE
4NA4Ligand/IonSODIUM ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
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:294BINDING SITE FOR RESIDUE BGC A 1001
02AC2SOFTWAREASP A:84 , GLY A:87 , SER A:88 , SER A:155 , ASP A:209 , GLY A:231 , THR A:232 , ASP A:413 , GLY A:414 , SER A:415 , GLY A:448 , SER A:449 , HOH A:1186 , HOH A:1196BINDING SITE FOR RESIDUE M6D 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:1123BINDING 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 , GLY A:896 , SER A:897 , HOH A:1123 , HOH A:1185BINDING SITE FOR RESIDUE M6D 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
07AC7SOFTWAREARG A:425 , ARG A:426 , LYS A:429 , HOH A:1234BINDING SITE FOR RESIDUE CIT A 1007
08AC8SOFTWARESER B:155 , PHE B:156 , PRO B:157 , THR B:172 , LYS B:173 , ASN B:208 , ASP B:209 , THR B:210 , ILE B:229 , ASN B:235 , GLU B:260 , GLN B:291 , GLU B:294 , HOH B:1204BINDING SITE FOR RESIDUE BGC B 1001
09AC9SOFTWAREASP 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:1140 , HOH B:1204BINDING SITE FOR RESIDUE M6D B 1002
10BC1SOFTWARESER 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:1164BINDING SITE FOR RESIDUE BGC B 1003
11BC2SOFTWAREASP B:532 , GLY B:535 , THR B:536 , 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:1164BINDING SITE FOR RESIDUE M6D B 1004
12BC3SOFTWARELEU B:242 , ILE B:245 , VAL B:248 , GLY B:250BINDING SITE FOR RESIDUE NA B 1005
13BC4SOFTWAREMET B:690 , VAL B:693 , VAL B:696 , GLY B:698BINDING SITE FOR RESIDUE NA B 1006
14BC5SOFTWAREARG B:425 , ARG B:426BINDING SITE FOR RESIDUE CIT B 1007

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FOE)

(-) Sequences/Alignments

Asymmetric/Biological 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 d4foea1 A:16-222 Mammalian type I hexokinase                                                                                                                                                                   d4foea2 A:223-465 Mammalian type I hexokinase                                                                                                                                                                                                      d4foea3 A:466-670 Mammalian type I hexokinase                                                                                                                                                                d4foea4 A:671-914 Mammalian type I hexokinase                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...........ee............eeeeeeee....eeeeeeeee....eeeeeeeeee..hhhhhh.hhhhhhhhhhhhhhhhhhh........eeeeee...ee.......ee...............hhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh..eeeeeee...eeeeeeee............eeeee.hhhhh..........hhhhhhhhhh........hhhhh...hhhhhhhhhhhhhhhh..hhhhh.hhhhhh....hhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeehhhhhhh.hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...........ee............eeeeeeee....eeeeeeeee.....eeeeeeeee..hhhhhh.hhhhhhhhhhhhhhhhhhhh.......eeeeee...eeeee..eeee...............hhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhh....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
                 4foe 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 d4foeb1 B:16-222 Mammalian type I hexokinase                                                                                                                                                                   d4foeb2 B:223-465 Mammalian type I hexokinase                                                                                                                                                                                                      d4foeb3 B:466-670 Mammalian type I hexokinase                                                                                                                                                                d4foeb4 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.....eeeeeee........eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee...ee.......ee...............hhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhh....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.hhh........eeeee.hhhhh..........hhhhhhhhhhh.......hhhhh...hhhhhhhhhhhhhhhh..hhhhh.hhhhhh....hhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeehhhhhhh.hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4foe 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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)

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  HXK1_HUMAN | P19367
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 Related Entries

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

UniProtKB/Swiss-Prot
        HXK1_HUMAN | P19367: 1cza 1dgk 1hkb 1hkc 1qha 4f9o 4foi 4fpa 4fpb

(-) Related Entries Specified in the PDB File

1hkb 4f9o 4foi 4fpa 4fpb