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1DQA
Asym. Unit
Info
Asym.Unit (269 KB)
Biol.Unit 1 (259 KB)
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(1)
Title
:
COMPLEX OF THE CATALYTIC PORTION OF HUMAN HMG-COA REDUCTASE WITH HMG, COA, AND NADP+
Authors
:
E. S. Istvan, M. Palnitkar, S. K. Buchanan, J. Deisenhofer
Date
:
30 Dec 99 (Deposition) - 08 Mar 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Oxidoreductase, Cholesterol Biosynthesis, Hmg-Coa, Nadph
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. S. Istvan, M. Palnitkar, S. K. Buchanan, J. Deisenhofer
Crystal Structure Of The Catalytic Portion Of Human Hmg-Coa Reductase: Insights Into Regulation Of Activity And Catalysis.
Embo J. V. 19 819 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 12)
Info
All Hetero Components
1a: COENZYME A (COAa)
1b: COENZYME A (COAb)
1c: COENZYME A (COAc)
1d: COENZYME A (COAd)
2a: 3-HYDROXY-3-METHYL-GLUTARIC ACID (MAHa)
2b: 3-HYDROXY-3-METHYL-GLUTARIC ACID (MAHb)
2c: 3-HYDROXY-3-METHYL-GLUTARIC ACID (MAHc)
2d: 3-HYDROXY-3-METHYL-GLUTARIC ACID (MAHd)
3a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
3b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
3c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
3d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
COA
4
Ligand/Ion
COENZYME A
2
MAH
4
Ligand/Ion
3-HYDROXY-3-METHYL-GLUTARIC ACID
3
NAP
4
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MAH A:201 , GLU A:559 , LEU A:562 , ALA A:564 , SER A:565 , ASN A:567 , ARG A:568 , ARG A:571 , VAL A:720 , LYS A:722 , HIS A:752 , ASN A:755 , SER A:852 , LEU A:853 , ALA A:856 , LEU A:862 , SER A:865 , HIS A:866 , HOH A:2178 , HOH A:2284 , HOH A:2290 , TYR B:479 , GLU B:528
BINDING SITE FOR RESIDUE COA A 101
02
AC2
SOFTWARE
TYR A:479 , GLU A:528 , MAH B:202 , GLU B:559 , LEU B:562 , ALA B:564 , SER B:565 , ASN B:567 , ARG B:568 , ARG B:571 , VAL B:720 , LYS B:722 , HIS B:752 , SER B:852 , LEU B:853 , SER B:865 , HIS B:866 , HOH B:2211 , HOH B:2279
BINDING SITE FOR RESIDUE COA B 102
03
AC3
SOFTWARE
LEU C:562 , ALA C:564 , SER C:565 , ASN C:567 , ARG C:568 , VAL C:720 , LYS C:722 , HIS C:752 , SER C:852 , LEU C:853 , LEU C:862 , SER C:865 , HIS C:866 , HOH C:2247 , HOH C:2248 , HOH C:2416 , MAH D:203 , TYR D:479 , GLU D:528
BINDING SITE FOR RESIDUE COA C 103
04
AC4
SOFTWARE
MAH C:204 , PRO C:477 , TYR C:479 , GLU D:559 , LEU D:562 , ALA D:564 , SER D:565 , ASN D:567 , ARG D:568 , ARG D:571 , VAL D:720 , LYS D:722 , HIS D:752 , ASN D:755 , SER D:852 , LEU D:853 , LEU D:862 , SER D:865 , HIS D:866 , HOH D:2265 , HOH D:2384
BINDING SITE FOR RESIDUE COA D 104
05
AC5
SOFTWARE
COA A:101 , GLU A:559 , LYS A:735 , ALA A:751 , ASN A:755 , HOH A:2062 , NAP B:2 , ARG B:590 , SER B:684 , ASP B:690 , LYS B:691 , LYS B:692
BINDING SITE FOR RESIDUE MAH A 201
06
AC6
SOFTWARE
ARG A:590 , SER A:626 , ARG A:627 , PHE A:628 , SER A:651 , GLY A:652 , ASP A:653 , ALA A:654 , MET A:655 , GLY A:656 , MET A:657 , ASN A:658 , MET A:659 , SER A:661 , ASP A:690 , LYS A:691 , ASP A:767 , GLY A:807 , ALA A:826 , HOH A:2168 , HOH A:2272 , MAH B:202 , GLU B:559 , HIS B:866 , HOH B:2155
BINDING SITE FOR RESIDUE NAP A 1
07
AC7
SOFTWARE
NAP A:1 , ARG A:590 , SER A:684 , ASP A:690 , LYS A:691 , LYS A:692 , COA B:102 , GLU B:559 , LYS B:735 , ALA B:751 , ASN B:755 , HIS B:866 , HOH B:2081
BINDING SITE FOR RESIDUE MAH B 202
08
AC8
SOFTWARE
MAH A:201 , GLU A:559 , HIS A:866 , ASN A:870 , HOH A:2288 , ARG B:590 , SER B:626 , ARG B:627 , PHE B:628 , SER B:651 , ASP B:653 , ALA B:654 , MET B:655 , GLY B:656 , MET B:657 , ASN B:658 , MET B:659 , SER B:661 , ASP B:690 , LYS B:691 , ASP B:767 , VAL B:805 , GLY B:806 , GLY B:807 , ALA B:826 , HOH B:2171 , HOH B:2266 , HOH B:2267 , HOH B:2268
BINDING SITE FOR RESIDUE NAP B 2
09
AC9
SOFTWARE
COA C:103 , GLU C:559 , LYS C:735 , ALA C:751 , ASN C:755 , NAP D:4 , ARG D:590 , SER D:684 , ASP D:690 , LYS D:691 , LYS D:692 , HOH D:2001
BINDING SITE FOR RESIDUE MAH D 203
10
BC1
SOFTWARE
MAH C:204 , ARG C:590 , SER C:626 , ARG C:627 , PHE C:628 , SER C:651 , GLY C:652 , ASP C:653 , ALA C:654 , MET C:655 , GLY C:656 , MET C:657 , ASN C:658 , MET C:659 , SER C:661 , ASP C:690 , LYS C:691 , ASP C:767 , GLY C:806 , GLY C:807 , ALA C:826 , HOH C:2111 , HOH C:2147 , HOH C:2166 , HOH C:2244 , HOH C:2273 , HOH C:2274 , HOH C:2452 , GLU D:559 , HIS D:866 , ASN D:870 , ARG D:871
BINDING SITE FOR RESIDUE NAP C 3
11
BC2
SOFTWARE
NAP C:3 , ARG C:590 , SER C:684 , ASP C:690 , LYS C:691 , LYS C:692 , HOH C:2005 , COA D:104 , GLU D:559 , LYS D:735 , ALA D:751 , ASN D:755
BINDING SITE FOR RESIDUE MAH C 204
12
BC3
SOFTWARE
GLU C:559 , HIS C:866 , ASN C:870 , ARG C:871 , HOH C:2095 , MAH D:203 , ARG D:590 , SER D:626 , ARG D:627 , PHE D:628 , SER D:651 , GLY D:652 , ASP D:653 , ALA D:654 , MET D:655 , GLY D:656 , MET D:657 , ASN D:658 , MET D:659 , SER D:661 , ASP D:690 , LYS D:691 , ASP D:767 , VAL D:805 , GLY D:806 , GLY D:807 , ALA D:826 , HOH D:2264 , HOH D:2269 , HOH D:2270 , HOH D:2453 , HOH D:2471
BINDING SITE FOR RESIDUE NAP D 4
[
close Site info
]
SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_011954 (I638V, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_011954
I
638
V
HMDH_HUMAN
Polymorphism
5908
A/B/C/D
I
638
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 14)
Info
All PROSITE Patterns/Profiles
1: HMG_COA_REDUCTASE_4 (A:464-870,B:464-866)
2: HMG_COA_REDUCTASE_1 (A:646-660,B:646-660,C:646-660,D:64...)
3: HMG_COA_REDUCTASE_2 (A:802-809,B:802-809,C:802-809,D:80...)
4: HMG_COA_REDUCTASE_3 (A:856-869,B:856-866,C:856-869,D:85...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HMG_COA_REDUCTASE_4
PS50065
Hydroxymethylglutaryl-coenzyme A reductases family profile.
HMDH_HUMAN
464-871
2
A:464-870
B:464-866
2
HMG_COA_REDUCTASE_1
PS00066
Hydroxymethylglutaryl-coenzyme A reductases signature 1.
HMDH_HUMAN
646-660
4
A:646-660
B:646-660
C:646-660
D:646-660
3
HMG_COA_REDUCTASE_2
PS00318
Hydroxymethylglutaryl-coenzyme A reductases signature 2.
HMDH_HUMAN
802-809
4
A:802-809
B:802-809
C:802-809
D:802-809
4
HMG_COA_REDUCTASE_3
PS01192
Hydroxymethylglutaryl-coenzyme A reductases signature 3.
HMDH_HUMAN
856-869
4
A:856-869
B:856-866
C:856-869
D:856-869
[
close PROSITE info
]
Exons
(9, 34)
Info
All Exons
Exon 1.14c (A:462-521 | B:462-521 | C:468-521 ...)
Exon 1.15b (A:522-574 | B:522-574 | C:522-574 ...)
Exon 1.15d (A:575-627 | B:575-627 | C:575-627 ...)
Exon 1.16a (A:627-662 | B:627-662 | C:627-662 ...)
Exon 1.17b (A:663-719 | B:663-719 | C:663-719 ...)
Exon 1.18a (A:720-766 | B:720-766 | C:720-766 ...)
Exon 1.19a (A:767-819 | B:767-819 | C:767-819 ...)
Exon 1.20b (A:820-870 | B:820-866 | C:820-871 ...)
Exon 1.21g (- | - | C:871-871 | D:871-872)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.13c/1.14c
02: Boundary 1.14c/1.15b
03: Boundary 1.15b/1.15d
04: Boundary 1.15d/1.16a
05: Boundary 1.16a/1.17b
06: Boundary 1.17b/1.18a
07: Boundary 1.18a/1.19a
08: Boundary 1.19a/1.20b
09: Boundary 1.20b/1.21g
10: Boundary 1.21g/-
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
1.2a
ENST00000287936
2a
ENSE00001378703
chr5:
74632993-74633125
133
HMDH_HUMAN
-
0
0
-
-
1.5b
ENST00000287936
5b
ENSE00002182886
chr5:
74638408-74638595
188
HMDH_HUMAN
1-55
55
0
-
-
1.6a
ENST00000287936
6a
ENSE00000753569
chr5:
74639678-74639789
112
HMDH_HUMAN
56-93
38
0
-
-
1.7b
ENST00000287936
7b
ENSE00000753572
chr5:
74640070-74640157
88
HMDH_HUMAN
93-122
30
0
-
-
1.8
ENST00000287936
8
ENSE00000753575
chr5:
74641399-74641483
85
HMDH_HUMAN
122-150
29
0
-
-
1.9
ENST00000287936
9
ENSE00000753578
chr5:
74643029-74643134
106
HMDH_HUMAN
151-186
36
0
-
-
1.10b
ENST00000287936
10b
ENSE00000753581
chr5:
74645867-74645973
107
HMDH_HUMAN
186-221
36
0
-
-
1.11
ENST00000287936
11
ENSE00000753584
chr5:
74646083-74646199
117
HMDH_HUMAN
222-260
39
0
-
-
1.12
ENST00000287936
12
ENSE00000753587
chr5:
74646614-74646774
161
HMDH_HUMAN
261-314
54
0
-
-
1.13a
ENST00000287936
13a
ENSE00000753589
chr5:
74646893-74647140
248
HMDH_HUMAN
314-397
84
0
-
-
1.13c
ENST00000287936
13c
ENSE00000753591
chr5:
74647249-74647427
179
HMDH_HUMAN
397-456
60
0
-
-
1.14c
ENST00000287936
14c
ENSE00000753593
chr5:
74650328-74650522
195
HMDH_HUMAN
457-521
65
4
A:462-521
B:462-521
C:468-521
D:477-521
60
60
54
45
1.15b
ENST00000287936
15b
ENSE00000753595
chr5:
74650881-74651039
159
HMDH_HUMAN
522-574
53
4
A:522-574
B:522-574
C:522-574
D:522-574
53
53
53
53
1.15d
ENST00000287936
15d
ENSE00000753597
chr5:
74651190-74651347
158
HMDH_HUMAN
575-627
53
4
A:575-627
B:575-627
C:575-627
D:575-627
53
53
53
53
1.16a
ENST00000287936
16a
ENSE00000753599
chr5:
74652168-74652273
106
HMDH_HUMAN
627-662
36
4
A:627-662
B:627-662
C:627-662
D:627-662
36
36
36
36
1.17b
ENST00000287936
17b
ENSE00000753601
chr5:
74654482-74654652
171
HMDH_HUMAN
663-719
57
4
A:663-719
B:663-719
C:663-719
D:663-719
57
57
57
57
1.18a
ENST00000287936
18a
ENSE00000753603
chr5:
74654995-74655135
141
HMDH_HUMAN
720-766
47
4
A:720-766
B:720-766
C:720-766
D:720-766
47
47
47
47
1.19a
ENST00000287936
19a
ENSE00000753605
chr5:
74655223-74655381
159
HMDH_HUMAN
767-819
53
4
A:767-819
B:767-819
C:767-819
D:767-819
53
53
53
53
1.20b
ENST00000287936
20b
ENSE00000753607
chr5:
74655810-74655964
155
HMDH_HUMAN
820-871
52
4
A:820-870
B:820-866
C:820-871
D:820-871
51
47
52
52
1.21g
ENST00000287936
21g
ENSE00001859900
chr5:
74656113-74657929
1817
HMDH_HUMAN
871-888
18
2
-
-
C:871-871
D:871-872
-
-
1
2
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1dqaa1 (A:587-703)
1b: SCOP_d1dqab1 (B:587-703)
1c: SCOP_d1dqac1 (C:587-703)
1d: SCOP_d1dqad1 (D:587-703)
2a: SCOP_d1dqaa4 (A:462-586,A:704-870)
2b: SCOP_d1dqab4 (B:462-586,B:704-866)
2c: SCOP_d1dqac4 (C:468-586,C:704-871)
2d: SCOP_d1dqad4 (D:477-586,D:704-872)
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)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
NAD-binding domain of HMG-CoA reductase
(20)
Family
:
NAD-binding domain of HMG-CoA reductase
(20)
Protein domain
:
NAD-binding domain of HMG-CoA reductase
(20)
Human (Homo sapiens) [TaxId: 9606]
(9)
1a
d1dqaa1
A:587-703
1b
d1dqab1
B:587-703
1c
d1dqac1
C:587-703
1d
d1dqad1
D:587-703
Fold
:
Substrate-binding domain of HMG-CoA reductase
(20)
Superfamily
:
Substrate-binding domain of HMG-CoA reductase
(20)
Family
:
Substrate-binding domain of HMG-CoA reductase
(20)
Protein domain
:
Substrate-binding domain of HMG-CoA reductase
(20)
Human (Homo sapiens) [TaxId: 9606]
(9)
2a
d1dqaa4
A:462-586,A:704-870
2b
d1dqab4
B:462-586,B:704-866
2c
d1dqac4
C:468-586,C:704-871
2d
d1dqad4
D:477-586,D:704-872
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1dqaA03 (A:587-703)
1b: CATH_1dqaC03 (C:587-703)
1c: CATH_1dqaD03 (D:587-703)
1d: CATH_1dqaB03 (B:587-703)
2a: CATH_1dqaB02 (B:537-585,B:704-866)
2b: CATH_1dqaA02 (A:537-585,A:704-870)
2c: CATH_1dqaC02 (C:537-585,C:704-870)
2d: CATH_1dqaD02 (D:537-585,D:704-870)
3a: CATH_1dqaC01 (C:468-536)
3b: CATH_1dqaB01 (B:462-536)
3c: CATH_1dqaD01 (D:477-536)
3d: CATH_1dqaA01 (A:462-536)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.420, no name defined]
(27)
Human (Homo sapiens)
(22)
1a
1dqaA03
A:587-703
1b
1dqaC03
C:587-703
1c
1dqaD03
D:587-703
1d
1dqaB03
B:587-703
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2
(27)
Homologous Superfamily
:
3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2
(27)
Human (Homo sapiens)
(22)
2a
1dqaB02
B:537-585,B:704-866
2b
1dqaA02
A:537-585,A:704-870
2c
1dqaC02
C:537-585,C:704-870
2d
1dqaD02
D:537-585,D:704-870
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
HMGR, N-terminal domain
(22)
Homologous Superfamily
:
HMGR, N-terminal domain
(22)
Human (Homo sapiens)
(22)
3a
1dqaC01
C:468-536
3b
1dqaB01
B:462-536
3c
1dqaD01
D:477-536
3d
1dqaA01
A:462-536
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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(currently selected atoms:
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Chain D
Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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