4FPB - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RECOMBINANT HUMAN HEXOKINASE TYPE I WITH 1,5-ANHYDROGLUCITOL 6-PHOSPHATE

Authors :   L. Shen, R. B. Honzatko

Date :   21 Jun 12 (Deposition) - 03 Jul 13 (Release) - 03 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Hexokinase, 1, 5-Anhydroglucitol 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

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

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 14)

No.	Name	Count	Type	Full Name
1	0WK	4	Ligand/Ion	1,5-ANHYDRO-6-O-PHOSPHONO-D-GLUCITOL
2	BGC	4	Ligand/Ion	BETA-D-GLUCOSE
3	CIT	2	Ligand/Ion	CITRIC ACID
4	NA	4	Ligand/Ion	SODIUM ION

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	0WK	4	Ligand/Ion	1,5-ANHYDRO-6-O-PHOSPHONO-D-GLUCITOL
2	BGC	4	Ligand/Ion	BETA-D-GLUCOSE
3	CIT	2	Ligand/Ion	CITRIC ACID
4	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	0WK	2	Ligand/Ion	1,5-ANHYDRO-6-O-PHOSPHONO-D-GLUCITOL
2	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
3	CIT	1	Ligand/Ion	CITRIC ACID
4	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (3, 5)

No.	Name	Count	Type	Full Name
1	0WK	2	Ligand/Ion	1,5-ANHYDRO-6-O-PHOSPHONO-D-GLUCITOL
2	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
3	CIT	1	Ligand/Ion	CITRIC ACID
4	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:155 , PHE A:156 , 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:1145	BINDING SITE FOR RESIDUE BGC A 1001
02	AC2	SOFTWARE	ASP A:84 , GLY A:87 , SER A:88 , THR A:153 , ASP A:209 , ILE A:229 , GLY A:231 , THR A:232 , ASP A:413 , GLY A:414 , SER A:415 , SER A:449	BINDING SITE FOR RESIDUE 0WK A 1002
03	AC3	SOFTWARE	SER 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	BINDING SITE FOR RESIDUE BGC A 1003
04	AC4	SOFTWARE	ASP 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	BINDING SITE FOR RESIDUE 0WK A 1004
05	AC5	SOFTWARE	LEU A:242 , ILE A:245 , VAL A:248 , GLY A:250	BINDING SITE FOR RESIDUE NA A 1005
06	AC6	SOFTWARE	MET A:690 , VAL A:693 , VAL A:696 , GLY A:698	BINDING SITE FOR RESIDUE NA A 1006
07	AC7	SOFTWARE	PHE A:380 , ARG A:425 , ARG A:426 , LYS A:429 , HOH A:1182	BINDING SITE FOR RESIDUE CIT A 1007
08	AC8	SOFTWARE	SER B:155 , PHE B:156 , 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	BINDING SITE FOR RESIDUE BGC B 1001
09	AC9	SOFTWARE	ASP B:84 , GLY B:87 , SER B:88 , ASP B:209 , ILE B:229 , GLY B:231 , THR B:232 , GLY B:414 , SER B:415 , SER B:449	BINDING SITE FOR RESIDUE 0WK B 1002
10	BC1	SOFTWARE	SER 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 , ASN B:683 , GLU B:708 , GLN B:739 , GLU B:742	BINDING SITE FOR RESIDUE BGC B 1003
11	BC2	SOFTWARE	ASP 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	BINDING SITE FOR RESIDUE 0WK B 1004
12	BC3	SOFTWARE	LEU B:242 , ILE B:245 , VAL B:248 , GLY B:250	BINDING SITE FOR RESIDUE NA B 1005
13	BC4	SOFTWARE	MET B:690 , VAL B:693 , VAL B:696 , GLY B:698	BINDING SITE FOR RESIDUE NA B 1006
14	BC5	SOFTWARE	GLN B:422 , ARG B:425 , ARG B:426	BINDING SITE FOR RESIDUE CIT B 1007

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

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

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

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

(no "Exon" information available for 4FPB)

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 d4fpba1 A:16-222 Mammalian type I hexokinase                                                                                                                                                                   d4fpba2 A:223-465 Mammalian type I hexokinase                                                                                                                                                                                                      d4fpba3 A:466-670 Mammalian type I hexokinase                                                                                                                                                                d4fpba4 A:671-914 Mammalian type I hexokinase                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhh....ee............eeeeeee.....eeeeeeeee....eeee....ee..hhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee....ee.......ee...............hhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh..eeeeeee...eeeeeeee.hhh........eeeee.hhhhh..........hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhh....hhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeehhhhhhh.hhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhh....ee............eeeeeeee....eeeeeeeee.....eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee...eeeee..eeee...............hhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh....eeeeeee...eeeeeeee............eeeee.hhhhh..........hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhh....hhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeehhhhhhh.hhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fpb 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 d4fpbb1 B:16-222 Mammalian type I hexokinase                                                                                                                                                                   d4fpbb2 B:223-465 Mammalian type I hexokinase                                                                                                                                                                                                      d4fpbb3 B:466-670 Mammalian type I hexokinase                                                                                                                                                                d4fpbb4 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....eeeeeeeeehhhheeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee...ee.......ee...............hhhhhhhhhhhh......eeeeeehhhhhhhhhhhhhh..eeeeeee...eeeeeeee.hhh........eeeee.hhhhh..........hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhh....hhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeehhhhhhh.hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhh....ee............eeeeeeee.....eeeeeeee.....eeeeeeee...hhhhhh.hhhhhhhhhhhhhhhhhhhh.......eeeeee...eeeee..eeee...............hhhhhhhhhhhh......eeeeeehhhhhhhhhhhh....eeeeeee...eeeeeeee............eeeee.hhhhh..........hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhh....hhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeehhhhhhh.hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fpb 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)
	-	→ 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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Ribonuclease H-like motif (1424)

Superfamily: Actin-like ATPase domain (426)

Family: Hexokinase (19)

Protein domain: Mammalian type I hexokinase (11)

Human (Homo sapiens) [TaxId: 9606] (10)

1a	d4fpba1	A:16-222
1b	d4fpba2	A:223-465
1c	d4fpba3	A:466-670
1d	d4fpba4	A:671-914
1e	d4fpbb1	B:16-222
1f	d4fpbb2	B:223-465
1g	d4fpbb3	B:466-670
1h	d4fpbb4	B:671-914

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4fpb)

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Access by PDB/NDB ID
	4fpb
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	HXK1_HUMAN \| P19367
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	HXK1_HUMAN \| P19367	:	1cza 1dgk 1hkb 1hkc 1qha 4f9o 4foe 4foi 4fpa

Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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