PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3MP3
Asym. Unit
Info
Asym.Unit (279 KB)
Biol.Unit 1 (97 KB)
Biol.Unit 2 (93 KB)
Biol.Unit 3 (94 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN LYASE IN COMPLEX WITH INHIBITOR HG-COA
Authors
:
Z. Fu, J. A. Runquist, C. Montgomery, H. M. Miziorko, J. -J. P. Kim
Date
:
24 Apr 10 (Deposition) - 16 Jun 10 (Release) - 24 Nov 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Keywords
:
Ketogenic Enzyme, Human Hmg-Coa Lyase, 3-Hydroxylglutaryl-Coa, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Fu, J. A. Runquist, C. Montgomery, H. M. Miziorko, J. J. Kim
Functional Insights Into Human Hmg-Coa Lyase From Structure Of Acyl-Coa-Containing Ternary Complexes.
J. Biol. Chem. V. 285 26341 2010
[
close entry info
]
Hetero Components
(3, 8)
Info
All Hetero Components
1a: 3-HYDROXYPENTANEDIOIC ACID (3HGa)
2a: (3R,5S,9R,21S)-1-[(2R,3S,4R,5R)-5-... (HGGa)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3HG
1
Ligand/Ion
3-HYDROXYPENTANEDIOIC ACID
2
HGG
1
Ligand/Ion
(3R,5S,9R,21S)-1-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-3,5,9,21-TETRAHYDROXY-8,8-DIMETHYL-10,14,19-TRIOXO-2,4,6-TRIOXA-18-THIA-11,15-DIAZA-3,5-DIPHOSPHATRICOSAN-23-OIC ACID 3,5-DIOXIDE
3
MG
6
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:41 , ASP A:42 , GLN A:45 , PHE A:127 , HIS A:233 , MG A:403 , HOH A:802
BINDING SITE FOR RESIDUE 3HG A 400
2
AC2
SOFTWARE
ASP A:42 , HIS A:233 , HIS A:235 , ASN A:275 , 3HG A:400
BINDING SITE FOR RESIDUE MG A 403
3
AC3
SOFTWARE
ARG B:41 , ASP B:42 , GLN B:45 , PHE B:76 , VAL B:77 , SER B:78 , TRP B:81 , PRO B:108 , ASN B:109 , LYS B:111 , GLY B:112 , ASN B:138 , ILE B:139 , ASN B:140 , ARG B:149 , TYR B:167 , SER B:169 , THR B:205 , HIS B:233 , MG B:401 , HOH B:695 , HOH B:861
BINDING SITE FOR RESIDUE HGG B 399
4
AC4
SOFTWARE
ASP B:42 , HIS B:233 , HIS B:235 , HGG B:399 , HOH B:992
BINDING SITE FOR RESIDUE MG B 401
5
AC5
SOFTWARE
ASP C:42 , HIS C:233 , HIS C:235 , ASN C:275
BINDING SITE FOR RESIDUE MG C 404
6
AC6
SOFTWARE
ASP D:42 , HIS D:233 , HIS D:235 , HOH D:684
BINDING SITE FOR RESIDUE MG D 405
7
AC7
SOFTWARE
ASP E:42 , HIS E:233 , HIS E:235 , ASN E:275
BINDING SITE FOR RESIDUE MG E 402
8
AC8
SOFTWARE
ASP F:42 , HIS F:233 , HIS F:235
BINDING SITE FOR RESIDUE MG F 406
[
close Site info
]
SAPs(SNPs)/Variants
(19, 114)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_058440 (E37K, chain A/B/C/D/E/F, )
02: VAR_003744 (R41Q, chain A/B/C/D/E/F, )
03: VAR_003745 (D42E, chain A/B/C/D/E/F, )
04: VAR_003746 (D42G, chain A/B/C/D/E/F, )
05: VAR_003747 (D42H, chain A/B/C/D/E/F, )
06: VAR_058441 (K48N, chain A/B/C/D/E/F, )
07: VAR_003748 (V70L, chain A/B/C/D/E/F, )
08: VAR_058442 (S75R, chain A/B/C/D/E/F, )
09: VAR_058443 (S142F, chain A/B/C/D/E/F, )
10: VAR_065453 (R165Q, chain A/B/C/D/E/F, )
11: VAR_058444 (C174Y, chain A/B/C/D/E/F, )
12: VAR_058445 (F192S, chain A/B/C/D/E/F, )
13: VAR_058446 (I200F, chain A/B/C/D/E/F, )
14: VAR_058447 (S201Y, chain A/B/C/D/E/F, )
15: VAR_058448 (G203E, chain A/B/C/D/E/F, )
16: VAR_058449 (D204N, chain A/B/C/D/E/F, )
17: VAR_003749 (H233R, chain A/B/C/D/E/F, )
18: VAR_058450 (L263P, chain A/B/C/D/E/F, )
19: VAR_014202 (E279K, chain A/B/C/D/E/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_058440
E
37
K
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
E
37
K
02
UniProt
VAR_003744
R
41
Q
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
R
41
Q
03
UniProt
VAR_003745
D
42
E
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
D
42
E
04
UniProt
VAR_003746
D
42
G
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
D
42
G
05
UniProt
VAR_003747
D
42
H
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
D
42
H
06
UniProt
VAR_058441
K
48
N
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
K
48
N
07
UniProt
VAR_003748
V
70
L
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
V
70
L
08
UniProt
VAR_058442
S
75
R
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
S
75
R
09
UniProt
VAR_058443
S
142
F
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
S
142
F
10
UniProt
VAR_065453
R
165
Q
HMGCL_HUMAN
Disease (HMGCLD)
199587895
A/B/C/D/E/F
R
165
Q
11
UniProt
VAR_058444
C
174
Y
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
C
174
Y
12
UniProt
VAR_058445
F
192
S
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
F
192
S
13
UniProt
VAR_058446
I
200
F
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
I
200
F
14
UniProt
VAR_058447
S
201
Y
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
S
201
Y
15
UniProt
VAR_058448
G
203
E
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
G
203
E
16
UniProt
VAR_058449
D
204
N
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
D
204
N
17
UniProt
VAR_003749
H
233
R
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
H
233
R
18
UniProt
VAR_058450
L
263
P
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B/C/D/E/F
L
263
P
19
UniProt
VAR_014202
E
279
K
HMGCL_HUMAN
Disease (HMGCLD)
28934894
A/B/C/D/E/F
E
279
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: PYR_CT (A:33-300,B:33-300,C:33-300,D:33-30...)
2: HMG_COA_LYASE (A:259-268,B:259-268,C:259-268,D:25...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PYR_CT
PS50991
Pyruvate carboxyltransferase domain.
HMGCL_HUMAN
33-300
6
A:33-300
B:33-300
C:33-300
D:33-300
E:33-300
F:33-300
2
HMG_COA_LYASE
PS01062
Hydroxymethylglutaryl-coenzyme A lyase active site.
HMGCL_HUMAN
259-268
6
A:259-268
B:259-268
C:259-268
D:259-264
E:259-268
F:259-268
[
close PROSITE info
]
Exons
(8, 48)
Info
All Exons
Exon 1.5 (A:28-48 | B:28-48 | C:28-48 | D:28...)
Exon 1.6a (A:49-84 | B:49-84 | C:49-84 | D:49...)
Exon 1.7a (A:85-116 | B:85-116 | C:85-116 | D...)
Exon 1.8a (A:117-166 | B:117-166 | C:117-166 ...)
Exon 1.9a (A:166-187 | B:166-187 | C:166-187 ...)
Exon 1.10a (A:188-250 | B:188-250 | C:188-250 ...)
Exon 1.13a (A:251-292 | B:251-292 | C:251-292 ...)
Exon 1.14c (A:293-323 | B:293-323 | C:293-323 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3a/1.5
2: Boundary 1.5/1.6a
3: Boundary 1.6a/1.7a
4: Boundary 1.7a/1.8a
5: Boundary 1.8a/1.9a
6: Boundary 1.9a/1.10a
7: Boundary 1.10a/1.13a
8: Boundary 1.13a/1.14c
9: Boundary 1.14c/-
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
1.3a
ENST00000374490
3a
ENSE00001600452
chr1:
24151949-24151846
104
HMGCL_HUMAN
1-20
20
0
-
-
1.5
ENST00000374490
5
ENSE00001663468
chr1:
24147083-24147000
84
HMGCL_HUMAN
21-48
28
6
A:28-48
B:28-48
C:28-48
D:28-48
E:28-48
F:28-48
21
21
21
21
21
21
1.6a
ENST00000374490
6a
ENSE00001745098
chr1:
24144073-24143966
108
HMGCL_HUMAN
49-84
36
6
A:49-84
B:49-84
C:49-84
D:49-84
E:49-84
F:49-84
36
36
36
36
36
36
1.7a
ENST00000374490
7a
ENSE00001639422
chr1:
24143260-24143165
96
HMGCL_HUMAN
85-116
32
6
A:85-116
B:85-116
C:85-116
D:85-116
E:85-116
F:85-116
32
32
32
32
32
32
1.8a
ENST00000374490
8a
ENSE00000758310
chr1:
24140828-24140680
149
HMGCL_HUMAN
117-166
50
6
A:117-166
B:117-166
C:117-166
D:117-166
E:117-166
F:117-166
50
50
50
50
50
50
1.9a
ENST00000374490
9a
ENSE00000758311
chr1:
24137289-24137226
64
HMGCL_HUMAN
166-187
22
6
A:166-187
B:166-187
C:166-187
D:166-187
E:166-187
F:166-187
22
22
22
22
22
22
1.10a
ENST00000374490
10a
ENSE00000758312
chr1:
24134813-24134625
189
HMGCL_HUMAN
188-250
63
6
A:188-250
B:188-250
C:188-250
D:188-250
E:188-250
F:188-250
63
63
63
63
63
63
1.13a
ENST00000374490
13a
ENSE00000758313
chr1:
24131015-24130890
126
HMGCL_HUMAN
251-292
42
6
A:251-292
B:251-292
C:251-292
D:251-292 (gaps)
E:251-292
F:251-292
42
42
42
42
42
42
1.14c
ENST00000374490
14c
ENSE00001463651
chr1:
24129054-24128375
680
HMGCL_HUMAN
293-325
33
6
A:293-323
B:293-323
C:293-323
D:293-323
E:293-323
F:293-323
31
31
31
31
31
31
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_HMGL_like_3mp3F01 (F:41-289)
1b: PFAM_HMGL_like_3mp3F02 (F:41-289)
1c: PFAM_HMGL_like_3mp3F03 (F:41-289)
1d: PFAM_HMGL_like_3mp3F04 (F:41-289)
1e: PFAM_HMGL_like_3mp3F05 (F:41-289)
1f: PFAM_HMGL_like_3mp3F06 (F:41-289)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
HMGL-like
(13)
Homo sapiens (Human)
(3)
1a
HMGL-like-3mp3F01
F:41-289
1b
HMGL-like-3mp3F02
F:41-289
1c
HMGL-like-3mp3F03
F:41-289
1d
HMGL-like-3mp3F04
F:41-289
1e
HMGL-like-3mp3F05
F:41-289
1f
HMGL-like-3mp3F06
F:41-289
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (279 KB)
Header - Asym.Unit
Biol.Unit 1 (97 KB)
Header - Biol.Unit 1
Biol.Unit 2 (93 KB)
Header - Biol.Unit 2
Biol.Unit 3 (94 KB)
Header - Biol.Unit 3
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
3MP3
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
