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1HKB
Asym. Unit
Info
Asym.Unit (298 KB)
Biol.Unit 1 (148 KB)
Biol.Unit 2 (149 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RECOMBINANT HUMAN BRAIN HEXOKINASE TYPE I COMPLEXED WITH GLUCOSE AND GLUCOSE-6-PHOSPHATE
Authors
:
A. E. Aleshin, C. Zeng, G. P. Burenkov, H. D. Bartunik, H. J. Fromm, R. B. Honzatko
Date
:
01 Dec 97 (Deposition) - 03 Jun 98 (Release) - 04 Aug 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Phosphotransferase, Glycolysis, Allosteric Enzyme, Glucose, Glucose-6-Phosphate
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. E. Aleshin, C. Zeng, G. P. Bourenkov, H. D. Bartunik, H. J. Fromm, R. B. Honzatko
The Mechanism Of Regulation Of Hexokinase: New Insights From The Crystal Structure Of Recombinant Human Brain Hexokinase Complexed With Glucose And Glucose-6-Phosphate.
Structure V. 6 39 1998
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
1b: BETA-D-GLUCOSE (BGCb)
1c: BETA-D-GLUCOSE (BGCc)
1d: BETA-D-GLUCOSE (BGCd)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: ALPHA-D-GLUCOSE-6-PHOSPHATE (G6Pa)
3b: ALPHA-D-GLUCOSE-6-PHOSPHATE (G6Pb)
3c: ALPHA-D-GLUCOSE-6-PHOSPHATE (G6Pc)
3d: ALPHA-D-GLUCOSE-6-PHOSPHATE (G6Pd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
4
Ligand/Ion
BETA-D-GLUCOSE
2
CA
4
Ligand/Ion
CALCIUM ION
3
G6P
4
Ligand/Ion
ALPHA-D-GLUCOSE-6-PHOSPHATE
[
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Sites
(12, 12)
Info
All Sites
01: 6CA (UNKNOWN)
02: 6CB (UNKNOWN)
03: 6NA (UNKNOWN)
04: 6NB (UNKNOWN)
05: GCA (UNKNOWN)
06: GCB (UNKNOWN)
07: GNA (UNKNOWN)
08: GNB (UNKNOWN)
09: MCA (UNKNOWN)
10: MCB (UNKNOWN)
11: MNA (UNKNOWN)
12: MNB (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
6CA
UNKNOWN
SER A:603 , ASP A:657 , SER A:897 , ASP A:532 , ASP A:861 , THR A:863 , THR A:680 , THR A:536
GLUCOSE-6-PHOSPHATE BINDING SITE IN C- TERMINAL DOMAIN.
02
6CB
UNKNOWN
SER B:603 , ASP B:657 , SER B:897 , ASP B:532 , ASP B:861 , THR B:863 , THR B:680 , THR B:536
GLUCOSE-6-PHOSPHATE BINDING SITE IN C- TERMINAL DOMAIN.
03
6NA
UNKNOWN
SER A:155 , ASP A:209 , SER A:449 , ASP A:84 , ASP A:413 , SER A:415 , ILE A:230 , SER A:88
GLUCOSE-6-PHOSPHATE BINDING SITE IN N- TERMINAL DOMAIN.
04
6NB
UNKNOWN
SER B:155 , ASP B:209 , SER B:449 , ASP B:84 , ASP B:413 , SER B:415 , ILE B:230 , SER B:88
GLUCOSE-6-PHOSPHATE BINDING SITE IN N- TERMINAL DOMAIN.
05
GCA
UNKNOWN
GLU A:742 , THR A:620 , GLU A:708 , ASN A:656 , ASP A:657 , ASN A:683 , LYS A:621
GLUCOSE BINDING SITE IN C-TERMINAL DOMAIN.
06
GCB
UNKNOWN
GLU B:742 , THR B:620 , GLU B:708 , ASN B:656 , ASP B:657 , ASN B:683 , LYS B:621
GLUCOSE BINDING SITE IN C-TERMINAL DOMAIN.
07
GNA
UNKNOWN
GLU A:294 , THR A:172 , GLU A:260 , ASN A:208 , ASP A:209 , ASN A:235 , LYS A:173
GLUCOSE BINDING SITE IN N-TERMINAL DOMAIN.
08
GNB
UNKNOWN
GLU B:294 , THR B:172 , GLU B:260 , ASN B:208 , ASP B:209 , ASN B:235 , LYS B:173
GLUCOSE BINDING SITE IN N-TERMINAL DOMAIN.
09
MCA
UNKNOWN
MET A:690 , VAL A:693 , VAL A:696 , GLY A:698
METAL ION BINDING SITE IN C-TERMINAL DOMAIN.
10
MCB
UNKNOWN
MET B:690 , VAL B:693 , VAL B:696 , GLY B:698
METAL ION BINDING SITE IN C-TERMINAL DOMAIN.
11
MNA
UNKNOWN
LEU A:242 , ILE A:245 , VAL A:248 , GLY A:250
METAL ION BINDING SITE IN N-TERMINAL DOMAIN.
12
MNB
UNKNOWN
LEU B:242 , ILE B:245 , VAL B:248 , GLY B:250
METAL ION BINDING SITE IN N-TERMINAL DOMAIN.
[
close Site info
]
SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_009878 (L529S, chain A/B, )
2: VAR_023780 (T680S, chain A/B, )
3: VAR_023781 (L776M, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_009878
L
529
S
HXK1_HUMAN
Disease (HK deficiency)
---
A/B
L
529
S
2
UniProt
VAR_023780
T
680
S
HXK1_HUMAN
Disease (HK deficiency)
---
A/B
T
680
S
3
UniProt
VAR_023781
L
776
M
HXK1_HUMAN
Polymorphism
1054203
A/B
L
776
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: HEXOKINASE_2 (A:16-458,B:16-458|A:464-906,B:464-...)
2: HEXOKINASE_1 (A:150-175,B:150-175|A:598-623,B:59...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HEXOKINASE_2
PS51748
Hexokinase domain profile.
HXK1_HUMAN
16-458
464-906
4
A:16-458
B:16-458
A:464-906
B:464-906
2
HEXOKINASE_1
PS00378
Hexokinase domain signature.
HXK1_HUMAN
150-175
598-623
4
A:150-175
B:150-175
A:598-623
B:598-623
[
close PROSITE info
]
Exons
(18, 36)
Info
All Exons
Exon 1.11 (A:16-21 | B:16-21)
Exon 1.15c (A:22-76 | B:22-76)
Exon 1.16b (A:76-125 | B:76-125)
Exon 1.17c (A:126-165 | B:126-165)
Exon 1.18 (A:166-197 | B:166-197)
Exon 1.19 (A:198-231 | B:198-231)
Exon 1.20b (A:231-292 | B:231-292)
Exon 1.21b (A:292-344 | B:292-344)
Exon 1.22 (A:344-422 | B:344-422)
Exon 1.23 (A:422-524 | B:422-524)
Exon 1.24a (A:524-573 | B:524-573)
Exon 1.24c (A:574-613 | B:574-613)
Exon 1.25a (A:614-645 | B:614-645)
Exon 1.26 (A:646-679 | B:646-679)
Exon 1.27b (A:679-740 | B:679-740)
Exon 1.28 (A:740-792 | B:740-792)
Exon 1.29 (A:792-870 | B:792-870)
Exon 1.30c (A:870-914 | B:870-914)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.11
02: Boundary 1.11/1.15c
03: Boundary 1.15c/1.16b
04: Boundary 1.16b/1.17c
05: Boundary 1.17c/1.18
06: Boundary 1.18/1.19
07: Boundary 1.19/1.20b
08: Boundary 1.20b/1.21b
09: Boundary 1.21b/1.22
10: Boundary 1.22/1.23
11: Boundary 1.23/1.24a
12: Boundary 1.24a/1.24c
13: Boundary 1.24c/1.25a
14: Boundary 1.25a/1.26
15: Boundary 1.26/1.27b
16: Boundary 1.27b/1.28
17: Boundary 1.28/1.29
18: Boundary 1.29/1.30c
19: Boundary 1.30c/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.11
ENST00000359426
11
ENSE00001460188
chr10:
71078600-71078766
167
HXK1_HUMAN
1-21
21
2
A:16-21
B:16-21
6
6
1.15c
ENST00000359426
15c
ENSE00001746665
chr10:
71103583-71103745
163
HXK1_HUMAN
22-76
55
2
A:22-76
B:22-76
55
55
1.16b
ENST00000359426
16b
ENSE00001199105
chr10:
71119653-71119801
149
HXK1_HUMAN
76-125
50
2
A:76-125
B:76-125
50
50
1.17c
ENST00000359426
17c
ENSE00001145342
chr10:
71124539-71124658
120
HXK1_HUMAN
126-165
40
2
A:126-165
B:126-165
40
40
1.18
ENST00000359426
18
ENSE00001145338
chr10:
71128292-71128387
96
HXK1_HUMAN
166-197
32
2
A:166-197
B:166-197
32
32
1.19
ENST00000359426
19
ENSE00001145331
chr10:
71128993-71129092
100
HXK1_HUMAN
198-231
34
2
A:198-231
B:198-231
34
34
1.20b
ENST00000359426
20b
ENSE00002165681
chr10:
71129197-71129380
184
HXK1_HUMAN
231-292
62
2
A:231-292
B:231-292
62
62
1.21b
ENST00000359426
21b
ENSE00001145318
chr10:
71136690-71136845
156
HXK1_HUMAN
292-344
53
2
A:292-344
B:292-344
53
53
1.22
ENST00000359426
22
ENSE00001145251
chr10:
71139618-71139851
234
HXK1_HUMAN
344-422
79
2
A:344-422
B:344-422
79
79
1.23
ENST00000359426
23
ENSE00001145307
chr10:
71142243-71142547
305
HXK1_HUMAN
422-524
103
2
A:422-524
B:422-524
103
103
1.24a
ENST00000359426
24a
ENSE00001145304
chr10:
71144089-71144237
149
HXK1_HUMAN
524-573
50
2
A:524-573
B:524-573
50
50
1.24c
ENST00000359426
24c
ENSE00001276961
chr10:
71144552-71144671
120
HXK1_HUMAN
574-613
40
2
A:574-613
B:574-613
40
40
1.25a
ENST00000359426
25a
ENSE00001276429
chr10:
71146079-71146174
96
HXK1_HUMAN
614-645
32
2
A:614-645
B:614-645
32
32
1.26
ENST00000359426
26
ENSE00001755911
chr10:
71148953-71149052
100
HXK1_HUMAN
646-679
34
2
A:646-679
B:646-679
34
34
1.27b
ENST00000359426
27b
ENSE00001145280
chr10:
71151881-71152064
184
HXK1_HUMAN
679-740
62
2
A:679-740
B:679-740
62
62
1.28
ENST00000359426
28
ENSE00001615072
chr10:
71154706-71154861
156
HXK1_HUMAN
740-792
53
2
A:740-792
B:740-792
53
53
1.29
ENST00000359426
29
ENSE00001145266
chr10:
71158351-71158584
234
HXK1_HUMAN
792-870
79
2
A:792-870
B:792-870
79
79
1.30c
ENST00000359426
30c
ENSE00001815320
chr10:
71160747-71161638
892
HXK1_HUMAN
870-917
48
2
A:870-914
B:870-914
45
45
[
close EXON info
]
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1hkba1 (A:16-222)
1b: SCOP_d1hkba2 (A:223-465)
1c: SCOP_d1hkba3 (A:466-670)
1d: SCOP_d1hkba4 (A:671-914)
1e: SCOP_d1hkbb1 (B:16-222)
1f: SCOP_d1hkbb2 (B:223-465)
1g: SCOP_d1hkbb3 (B:466-670)
1h: SCOP_d1hkbb4 (B:671-914)
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(
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(
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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
d1hkba1
A:16-222
1b
d1hkba2
A:223-465
1c
d1hkba3
A:466-670
1d
d1hkba4
A:671-914
1e
d1hkbb1
B:16-222
1f
d1hkbb2
B:223-465
1g
d1hkbb3
B:466-670
1h
d1hkbb4
B:671-914
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1hkbA03 (A:513-670,A:894-914)
1b: CATH_1hkbB03 (B:513-670,B:894-914)
1c: CATH_1hkbA01 (A:54-222,A:446-463)
1d: CATH_1hkbB01 (B:54-222,B:446-463)
2a: CATH_1hkbA02 (A:16-53,A:223-445)
2b: CATH_1hkbB02 (B:16-53,B:223-445)
2c: CATH_1hkbA04 (A:481-512,A:671-892)
2d: CATH_1hkbB04 (B:481-512,B:671-892)
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(
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.40, no name defined]
(217)
Human (Homo sapiens)
(36)
1a
1hkbA03
A:513-670,A:894-914
1b
1hkbB03
B:513-670,B:894-914
1c
1hkbA01
A:54-222,A:446-463
1d
1hkbB01
B:54-222,B:446-463
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Hexokinase; domain 1
(22)
Homologous Superfamily
:
[code=3.40.367.20, no name defined]
(22)
Human (Homo sapiens)
(16)
2a
1hkbA02
A:16-53,A:223-445
2b
1hkbB02
B:16-53,B:223-445
2c
1hkbA04
A:481-512,A:671-892
2d
1hkbB04
B:481-512,B:671-892
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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