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3MP3
Biol. Unit 1
Info
Asym.Unit (279 KB)
Biol.Unit 1 (97 KB)
Biol.Unit 2 (93 KB)
Biol.Unit 3 (94 KB)
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(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
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Hetero Components
(2, 2)
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
-1
Ligand/Ion
MAGNESIUM ION
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (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
[
close Site info
]
SAPs(SNPs)/Variants
(19, 38)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_058440 (E37K, chain A/B, )
02: VAR_003744 (R41Q, chain A/B, )
03: VAR_003745 (D42E, chain A/B, )
04: VAR_003746 (D42G, chain A/B, )
05: VAR_003747 (D42H, chain A/B, )
06: VAR_058441 (K48N, chain A/B, )
07: VAR_003748 (V70L, chain A/B, )
08: VAR_058442 (S75R, chain A/B, )
09: VAR_058443 (S142F, chain A/B, )
10: VAR_065453 (R165Q, chain A/B, )
11: VAR_058444 (C174Y, chain A/B, )
12: VAR_058445 (F192S, chain A/B, )
13: VAR_058446 (I200F, chain A/B, )
14: VAR_058447 (S201Y, chain A/B, )
15: VAR_058448 (G203E, chain A/B, )
16: VAR_058449 (D204N, chain A/B, )
17: VAR_003749 (H233R, chain A/B, )
18: VAR_058450 (L263P, chain A/B, )
19: VAR_014202 (E279K, chain A/B, )
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
E
37
K
02
UniProt
VAR_003744
R
41
Q
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
R
41
Q
03
UniProt
VAR_003745
D
42
E
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
D
42
E
04
UniProt
VAR_003746
D
42
G
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
D
42
G
05
UniProt
VAR_003747
D
42
H
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
D
42
H
06
UniProt
VAR_058441
K
48
N
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
K
48
N
07
UniProt
VAR_003748
V
70
L
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
V
70
L
08
UniProt
VAR_058442
S
75
R
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
S
75
R
09
UniProt
VAR_058443
S
142
F
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
S
142
F
10
UniProt
VAR_065453
R
165
Q
HMGCL_HUMAN
Disease (HMGCLD)
199587895
A/B
R
165
Q
11
UniProt
VAR_058444
C
174
Y
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
C
174
Y
12
UniProt
VAR_058445
F
192
S
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
F
192
S
13
UniProt
VAR_058446
I
200
F
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
I
200
F
14
UniProt
VAR_058447
S
201
Y
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
S
201
Y
15
UniProt
VAR_058448
G
203
E
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
G
203
E
16
UniProt
VAR_058449
D
204
N
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
D
204
N
17
UniProt
VAR_003749
H
233
R
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
H
233
R
18
UniProt
VAR_058450
L
263
P
HMGCL_HUMAN
Disease (HMGCLD)
---
A/B
L
263
P
19
UniProt
VAR_014202
E
279
K
HMGCL_HUMAN
Disease (HMGCLD)
28934894
A/B
E
279
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PYR_CT (A:33-300,B:33-300)
2: HMG_COA_LYASE (A:259-268,B:259-268)
;
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
2
A:33-300
B:33-300
-
-
-
-
2
HMG_COA_LYASE
PS01062
Hydroxymethylglutaryl-coenzyme A lyase active site.
HMGCL_HUMAN
259-268
2
A:259-268
B:259-268
-
-
-
-
[
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]
Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
[
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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)
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Clans
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)
(
)
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
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Asymmetric Unit 1
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