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4F7I
Asym. Unit
Info
Asym.Unit (469 KB)
Biol.Unit 1 (232 KB)
Biol.Unit 2 (232 KB)
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Title
:
STRUCTURE OF ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS THERMOPHILUS IN COMPLEX WITH IPM, MN AND NADH
Authors
:
A. Pallo, E. Graczer, P. Zavodszky, M. S. Weiss, M. Vas
Date
:
16 May 12 (Deposition) - 13 Jun 12 (Release) - 26 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Isopropylmalate Dehydrogenase, 3-Ipm-Dh, Beta-Ipm Dehydrogenase, Imdh, Ipmdh, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Pallo, J. Olah, E. Graczer, A. Merli, P. Zavodszky, M. S. Weiss, M. Va
Structural And Energetic Basis Of Isopropylmalate Dehydrogenase Enzyme Catalysis.
Febs J. V. 281 5063 2014
[
close entry info
]
Hetero Components
(7, 57)
Info
All Hetero Components
1a: ETHANOL (EOHa)
1b: ETHANOL (EOHb)
1c: ETHANOL (EOHc)
1d: ETHANOL (EOHd)
1e: ETHANOL (EOHe)
1f: ETHANOL (EOHf)
2a: GLYCEROL (GOLa)
2aa: GLYCEROL (GOLaa)
2ab: GLYCEROL (GOLab)
2ac: GLYCEROL (GOLac)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
2s: GLYCEROL (GOLs)
2t: GLYCEROL (GOLt)
2u: GLYCEROL (GOLu)
2v: GLYCEROL (GOLv)
2w: GLYCEROL (GOLw)
2x: GLYCEROL (GOLx)
2y: GLYCEROL (GOLy)
2z: GLYCEROL (GOLz)
3a: 3-ISOPROPYLMALIC ACID (IPMa)
3b: 3-ISOPROPYLMALIC ACID (IPMb)
3c: 3-ISOPROPYLMALIC ACID (IPMc)
3d: 3-ISOPROPYLMALIC ACID (IPMd)
4a: POTASSIUM ION (Ka)
4b: POTASSIUM ION (Kb)
4c: POTASSIUM ION (Kc)
4d: POTASSIUM ION (Kd)
4e: POTASSIUM ION (Ke)
4f: POTASSIUM ION (Kf)
4g: POTASSIUM ION (Kg)
5a: MANGANESE (II) ION (MNa)
5b: MANGANESE (II) ION (MNb)
5c: MANGANESE (II) ION (MNc)
5d: MANGANESE (II) ION (MNd)
6a: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOa)
6b: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOb)
6c: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOc)
7a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
7b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
7c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
7d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EOH
6
Ligand/Ion
ETHANOL
2
GOL
29
Ligand/Ion
GLYCEROL
3
IPM
4
Ligand/Ion
3-ISOPROPYLMALIC ACID
4
K
7
Ligand/Ion
POTASSIUM ION
5
MN
4
Ligand/Ion
MANGANESE (II) ION
6
MPO
3
Ligand/Ion
3[N-MORPHOLINO]PROPANE SULFONIC ACID
7
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(57, 57)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (SOFTWARE)
54: FC9 (SOFTWARE)
55: GC1 (SOFTWARE)
56: GC2 (SOFTWARE)
57: GC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:94 , ARG A:104 , ARG A:132 , TYR A:139 , ASP A:241 , NAD A:900 , MN A:999 , HOH A:2002 , HOH A:2022 , LYS B:185 , VAL B:188 , ASP B:217 , HOH B:2013
BINDING SITE FOR RESIDUE IPM A 800
02
AC2
SOFTWARE
ILE A:11 , SER A:71 , VAL A:72 , GLY A:73 , GLY A:74 , GLU A:87 , LEU A:90 , LEU A:254 , GLU A:270 , HIS A:273 , GLY A:274 , SER A:275 , ALA A:276 , PRO A:277 , ASP A:278 , ILE A:279 , ASN A:286 , IPM A:800 , K A:1001 , GOL A:1003 , GOL A:1005 , HOH A:2004 , HOH A:2006 , HOH A:2022 , HOH A:2023 , HOH A:2033 , HOH A:2044 , HOH A:2076 , HOH A:2086 , HOH A:2100 , ASN B:187 , TYR B:215 , ALA B:218 , HIS B:222
BINDING SITE FOR RESIDUE NAD A 900
03
AC3
SOFTWARE
LYS A:175 , ARG A:176 , GLU A:299 , HIS A:300 , GOL A:1009
BINDING SITE FOR RESIDUE MPO A 950
04
AC4
SOFTWARE
ASP A:241 , IPM A:800 , HOH A:2001 , HOH A:2002 , ASP B:217
BINDING SITE FOR RESIDUE MN A 999
05
AC5
SOFTWARE
GLY A:70 , SER A:71 , GLU A:270 , PRO A:271 , HIS A:273 , NAD A:900
BINDING SITE FOR RESIDUE K A 1001
06
AC6
SOFTWARE
GLU A:62 , ALA A:64 , THR A:266
BINDING SITE FOR RESIDUE K A 1002
07
AC7
SOFTWARE
GLY A:73 , GLY A:74 , TRP A:77 , ASP A:78 , ARG A:85 , GLU A:87 , NAD A:900 , TYR B:215
BINDING SITE FOR RESIDUE GOL A 1003
08
AC8
SOFTWARE
GLU A:155 , TYR A:157 , VAL A:183 , VAL A:191 , GLY A:192 , TRP A:195 , THR A:235 , GLY A:236 , PHE A:239 , HOH A:2018 , HOH A:2068
BINDING SITE FOR RESIDUE GOL A 1004
09
AC9
SOFTWARE
SER A:253 , LEU A:254 , ASP A:326 , NAD A:900 , HOH A:2100 , MET B:221 , ARG B:225 , HOH B:2038
BINDING SITE FOR RESIDUE GOL A 1005
10
BC1
SOFTWARE
LYS A:95 , GLY A:136 , GLY A:137 , ARG A:156 , GLU A:161 , HOH A:2039
BINDING SITE FOR RESIDUE GOL A 1006
11
BC2
SOFTWARE
LYS A:107 , VAL A:108 , PHE A:109 , LEU A:112 , PRO A:251 , LEU A:319 , GOL A:1008 , HOH A:2064
BINDING SITE FOR RESIDUE GOL A 1007
12
BC3
SOFTWARE
PRO A:105 , ALA A:106 , LYS A:107 , PHE A:109 , LEU A:256 , GOL A:1007 , GOL A:1009
BINDING SITE FOR RESIDUE GOL A 1008
13
BC4
SOFTWARE
ALA A:295 , MET A:296 , GLU A:299 , GLU A:312 , MPO A:950 , GOL A:1008
BINDING SITE FOR RESIDUE GOL A 1009
14
BC5
SOFTWARE
GLY A:263 , GOL A:1011
BINDING SITE FOR RESIDUE GOL A 1010
15
BC6
SOFTWARE
ARG A:164 , ARG A:167 , GLU A:171 , GOL A:1010
BINDING SITE FOR RESIDUE GOL A 1011
16
BC7
SOFTWARE
MET A:221 , ARG A:225 , SER B:253 , LEU B:254
BINDING SITE FOR RESIDUE EOH A 1012
17
BC8
SOFTWARE
LYS A:185 , ASP A:217 , HOH A:2013 , LEU B:91 , ARG B:94 , ARG B:104 , ARG B:132 , TYR B:139 , ASP B:241 , NAD B:900 , MN B:999 , HOH B:2021
BINDING SITE FOR RESIDUE IPM B 800
18
BC9
SOFTWARE
ASN A:187 , TYR A:215 , ALA A:218 , HOH A:2061 , ILE B:11 , SER B:71 , VAL B:72 , GLY B:73 , GLY B:74 , GLU B:87 , LEU B:90 , LEU B:254 , GLU B:270 , VAL B:272 , HIS B:273 , GLY B:274 , SER B:275 , ALA B:276 , PRO B:277 , ASP B:278 , ILE B:279 , ASN B:286 , IPM B:800 , K B:1001 , GOL B:1004 , HOH B:2009 , HOH B:2016 , HOH B:2021 , HOH B:2035 , HOH B:2044 , HOH B:2046
BINDING SITE FOR RESIDUE NAD B 900
19
CC1
SOFTWARE
ASP A:217 , ASP B:241 , IPM B:800 , HOH B:2001 , HOH B:2002
BINDING SITE FOR RESIDUE MN B 999
20
CC2
SOFTWARE
GLY B:70 , SER B:71 , GLU B:270 , PRO B:271 , HIS B:273 , NAD B:900
BINDING SITE FOR RESIDUE K B 1001
21
CC3
SOFTWARE
GLU B:62 , ALA B:64 , THR B:266 , HOH B:2050 , HOH B:2051
BINDING SITE FOR RESIDUE K B 1002
22
CC4
SOFTWARE
GLU B:155 , TYR B:157 , VAL B:183 , TRP B:195 , THR B:235 , GLY B:236 , PHE B:239 , HOH B:2037 , HOH B:2098
BINDING SITE FOR RESIDUE GOL B 1003
23
CC5
SOFTWARE
TYR A:215 , GLY B:73 , GLY B:74 , TRP B:77 , ASP B:78 , ARG B:85 , GLU B:87 , NAD B:900 , HOH B:2093 , HOH B:2108
BINDING SITE FOR RESIDUE GOL B 1004
24
CC6
SOFTWARE
PRO A:143 , ARG A:156 , ASP B:47 , LYS B:76 , TRP B:77 , LEU B:80 , PRO B:143 , TRP B:152 , HOH B:2024
BINDING SITE FOR RESIDUE GOL B 1005
25
CC7
SOFTWARE
LYS B:107 , VAL B:108 , PHE B:109 , PRO B:251 , GOL B:1007 , HOH B:2057
BINDING SITE FOR RESIDUE GOL B 1006
26
CC8
SOFTWARE
PRO B:105 , ALA B:106 , LYS B:107 , LEU B:256 , LEU B:257 , LEU B:292 , GOL B:1006 , GOL B:1008
BINDING SITE FOR RESIDUE GOL B 1007
27
CC9
SOFTWARE
PRO B:105 , ALA B:295 , MET B:296 , GLU B:312 , GOL B:1007
BINDING SITE FOR RESIDUE GOL B 1008
28
DC1
SOFTWARE
PRO B:7 , PRO B:13 , GLU B:17
BINDING SITE FOR RESIDUE EOH B 1009
29
DC2
SOFTWARE
GLU B:200 , GLY B:203 , TYR B:206 , VAL B:209 , LEU B:211 , HOH B:2080 , HOH B:2117
BINDING SITE FOR RESIDUE GOL B 1010
30
DC3
SOFTWARE
LEU C:90 , LEU C:91 , ARG C:94 , ARG C:104 , ARG C:132 , TYR C:139 , ASP C:241 , NAD C:900 , MN C:999 , HOH C:2001 , HOH C:2014 , LYS D:185 , VAL D:188 , ASP D:217 , HOH D:2007
BINDING SITE FOR RESIDUE IPM C 800
31
DC4
SOFTWARE
ILE C:11 , SER C:71 , VAL C:72 , GLY C:73 , GLY C:74 , GLU C:87 , LEU C:90 , LEU C:254 , GLU C:270 , VAL C:272 , HIS C:273 , GLY C:274 , SER C:275 , ALA C:276 , PRO C:277 , ASP C:278 , ILE C:279 , ASN C:286 , IPM C:800 , K C:1001 , GOL C:1004 , HOH C:2004 , HOH C:2011 , HOH C:2014 , HOH C:2031 , HOH C:2056 , HOH C:2057 , ASN D:187 , TYR D:215 , ALA D:218 , HOH D:2029
BINDING SITE FOR RESIDUE NAD C 900
32
DC5
SOFTWARE
LEU C:103 , LYS C:175 , ARG C:176 , MET C:296 , GLU C:299 , HIS C:300 , GOL C:1005
BINDING SITE FOR RESIDUE MPO C 950
33
DC6
SOFTWARE
ASP C:241 , IPM C:800 , HOH C:2001 , HOH C:2002 , ASP D:217
BINDING SITE FOR RESIDUE MN C 999
34
DC7
SOFTWARE
GLY C:70 , SER C:71 , GLU C:270 , PRO C:271 , HIS C:273 , NAD C:900
BINDING SITE FOR RESIDUE K C 1001
35
DC8
SOFTWARE
GLU C:62 , ALA C:64 , THR C:266 , HOH C:2098
BINDING SITE FOR RESIDUE K C 1002
36
DC9
SOFTWARE
GLU C:155 , TYR C:157 , VAL C:183 , VAL C:191 , GLY C:192 , TRP C:195 , THR C:235 , GLY C:236 , PHE C:239 , HOH C:2043 , HOH C:2044
BINDING SITE FOR RESIDUE GOL C 1003
37
EC1
SOFTWARE
GLY C:73 , GLY C:74 , TRP C:77 , ASP C:78 , ARG C:85 , GLU C:87 , NAD C:900 , HOH C:2087 , HOH C:2118 , TYR D:215
BINDING SITE FOR RESIDUE GOL C 1004
38
EC2
SOFTWARE
MET C:296 , GLU C:299 , GLU C:312 , MPO C:950 , GOL C:1006
BINDING SITE FOR RESIDUE GOL C 1005
39
EC3
SOFTWARE
PRO C:105 , LYS C:107 , PHE C:109 , PRO C:258 , GOL C:1005 , GOL C:1007
BINDING SITE FOR RESIDUE GOL C 1006
40
EC4
SOFTWARE
LYS C:107 , VAL C:108 , PHE C:109 , PRO C:251 , LEU C:292 , GOL C:1006 , HOH C:2075
BINDING SITE FOR RESIDUE GOL C 1007
41
EC5
SOFTWARE
GOL C:1008
BINDING SITE FOR RESIDUE GOL C 1018
42
EC6
SOFTWARE
GLU C:171 , ARG C:174 , GLY C:205 , ILE C:284 , SER C:330 , GOL C:1018 , HOH C:2109
BINDING SITE FOR RESIDUE GOL C 1008
43
EC7
SOFTWARE
GLU C:148 , HOH C:2110 , LYS D:159 , PHE D:194
BINDING SITE FOR RESIDUE EOH C 1009
44
EC8
SOFTWARE
GLY C:79 , LEU C:80 , ARG C:85 , HOH C:2118
BINDING SITE FOR RESIDUE EOH C 1010
45
EC9
SOFTWARE
LYS C:185 , ASP C:217 , HOH C:2017 , LEU D:90 , LEU D:91 , ARG D:94 , ARG D:104 , ARG D:132 , TYR D:139 , ASP D:241 , NAD D:900 , MN D:999 , HOH D:2002 , HOH D:2016
BINDING SITE FOR RESIDUE IPM D 800
46
FC1
SOFTWARE
ASN C:187 , TYR C:215 , ALA C:218 , HOH C:2027 , ILE D:11 , SER D:71 , VAL D:72 , GLY D:73 , GLY D:74 , GLU D:87 , LEU D:90 , LEU D:254 , GLU D:270 , HIS D:273 , GLY D:274 , SER D:275 , ALA D:276 , PRO D:277 , ASP D:278 , ILE D:279 , ASN D:286 , IPM D:800 , K D:1001 , GOL D:1004 , HOH D:2003 , HOH D:2006 , HOH D:2016 , HOH D:2021 , HOH D:2048 , HOH D:2067
BINDING SITE FOR RESIDUE NAD D 900
47
FC2
SOFTWARE
LEU D:103 , ALA D:172 , LYS D:175 , ARG D:176 , MET D:296 , GLU D:299 , HIS D:300 , GOL D:1007
BINDING SITE FOR RESIDUE MPO D 950
48
FC3
SOFTWARE
ASP C:217 , ASP D:241 , IPM D:800 , HOH D:2001 , HOH D:2002
BINDING SITE FOR RESIDUE MN D 999
49
FC4
SOFTWARE
GLY D:70 , SER D:71 , GLU D:270 , PRO D:271 , HIS D:273 , NAD D:900
BINDING SITE FOR RESIDUE K D 1001
50
FC5
SOFTWARE
GLU D:155 , TYR D:157 , VAL D:183 , VAL D:191 , GLY D:192 , TRP D:195 , THR D:235 , GLY D:236 , PHE D:239 , HOH D:2017 , HOH D:2036
BINDING SITE FOR RESIDUE GOL D 1003
51
FC6
SOFTWARE
TYR C:215 , GLY D:73 , GLY D:74 , TRP D:77 , ASP D:78 , ARG D:85 , GLU D:87 , NAD D:900 , HOH D:2066
BINDING SITE FOR RESIDUE GOL D 1004
52
FC7
SOFTWARE
ASP C:47 , LYS C:76 , TRP C:77 , LEU C:80 , PRO C:143 , TRP C:152 , PRO D:143 , THR D:154 , ARG D:156 , HOH D:2023
BINDING SITE FOR RESIDUE GOL D 1005
53
FC8
SOFTWARE
LYS D:107 , VAL D:108 , PHE D:109 , LEU D:112 , PRO D:251 , LEU D:319 , GOL D:1008 , HOH D:2057
BINDING SITE FOR RESIDUE GOL D 1006
54
FC9
SOFTWARE
MET D:296 , GLU D:299 , MPO D:950 , GOL D:1008
BINDING SITE FOR RESIDUE GOL D 1007
55
GC1
SOFTWARE
PRO D:105 , ALA D:106 , LYS D:107 , LEU D:256 , LEU D:257 , LEU D:292 , GOL D:1006 , GOL D:1007
BINDING SITE FOR RESIDUE GOL D 1008
56
GC2
SOFTWARE
SER C:253 , LEU C:254 , MET D:221 , ARG D:225
BINDING SITE FOR RESIDUE EOH D 1009
57
GC3
SOFTWARE
MET C:221 , SER D:253 , LEU D:254 , HOH D:2081 , HOH D:2082
BINDING SITE FOR RESIDUE EOH D 1010
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d4f7ia_ (A:)
1b: SCOP_d4f7ib_ (B:)
1c: SCOP_d4f7ic_ (C:)
1d: SCOP_d4f7id_ (D:)
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Protein Domains
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Organisms
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Isocitrate/Isopropylmalate dehydrogenase-like
(143)
Superfamily
:
Isocitrate/Isopropylmalate dehydrogenase-like
(143)
Family
:
Dimeric isocitrate & isopropylmalate dehydrogenases
(102)
Protein domain
:
automated matches
(45)
Thermus thermophilus HB8 [TaxId: 300852]
(1)
1a
d4f7ia_
A:
1b
d4f7ib_
B:
1c
d4f7ic_
C:
1d
d4f7id_
D:
[
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
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all PFAM domains
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Atom Selection
(currently selected atoms:
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Miscellaneous
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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)
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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") .
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