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4YB4
Asym. Unit
Info
Asym.Unit (234 KB)
Biol.Unit 1 (224 KB)
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Title
:
CRYSTAL STRUCTURE OF HOMOISOCITRATE DEHYDROGENASE FROM THERMUS THERMOPHILUS IN COMPLEX WITH HOMOISOCITRATE, MAGNESIUM ION (II) AND NADH
Authors
:
K. Takahashi, T. Tomita, T. Kuzuyama, M. Nishiyama
Date
:
18 Feb 15 (Deposition) - 09 Mar 16 (Release) - 09 Mar 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Homoisocitrate Dehydrogenase Thermus Thermophilus, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Takahashi, T. Tomita, T. Kuzuyama, M. Nishiyama
Structure Of Homoisocitrate Dehydrogenase From Thermus Thermophilus In Complex With Homoisocitrate, Magnesium(Ii) And Nadh
To Be Published
[
close entry info
]
Hetero Components
(5, 66)
Info
All Hetero Components
1a: (1R,2S)-1-HYDROXYBUTANE-1,2,4-TRIC... (48Ya)
1b: (1R,2S)-1-HYDROXYBUTANE-1,2,4-TRIC... (48Yb)
1c: (1R,2S)-1-HYDROXYBUTANE-1,2,4-TRIC... (48Yc)
1d: (1R,2S)-1-HYDROXYBUTANE-1,2,4-TRIC... (48Yd)
2a: GLYCEROL (GOLa)
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)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
4b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
4c: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIc)
4d: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAId)
5a: SULFATE ION (SO4a)
5aa: SULFATE ION (SO4aa)
5ab: SULFATE ION (SO4ab)
5ac: SULFATE ION (SO4ac)
5ad: SULFATE ION (SO4ad)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
5h: SULFATE ION (SO4h)
5i: SULFATE ION (SO4i)
5j: SULFATE ION (SO4j)
5k: SULFATE ION (SO4k)
5l: SULFATE ION (SO4l)
5m: SULFATE ION (SO4m)
5n: SULFATE ION (SO4n)
5o: SULFATE ION (SO4o)
5p: SULFATE ION (SO4p)
5q: SULFATE ION (SO4q)
5r: SULFATE ION (SO4r)
5s: SULFATE ION (SO4s)
5t: SULFATE ION (SO4t)
5u: SULFATE ION (SO4u)
5v: SULFATE ION (SO4v)
5w: SULFATE ION (SO4w)
5x: SULFATE ION (SO4x)
5y: SULFATE ION (SO4y)
5z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
48Y
4
Ligand/Ion
(1R,2S)-1-HYDROXYBUTANE-1,2,4-TRICARBOXYLIC ACID
2
GOL
24
Ligand/Ion
GLYCEROL
3
MG
4
Ligand/Ion
MAGNESIUM ION
4
NAI
4
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
5
SO4
30
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(66, 66)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
29: AF2 (SOFTWARE)
30: AF3 (SOFTWARE)
31: AF4 (SOFTWARE)
32: AF5 (SOFTWARE)
33: AF6 (SOFTWARE)
34: AF7 (SOFTWARE)
35: AF8 (SOFTWARE)
36: AF9 (SOFTWARE)
37: AG1 (SOFTWARE)
38: AG2 (SOFTWARE)
39: AG3 (SOFTWARE)
40: AG4 (SOFTWARE)
41: AG5 (SOFTWARE)
42: AG6 (SOFTWARE)
43: AG7 (SOFTWARE)
44: AG8 (SOFTWARE)
45: AG9 (SOFTWARE)
46: AH1 (SOFTWARE)
47: AH2 (SOFTWARE)
48: AH3 (SOFTWARE)
49: AH4 (SOFTWARE)
50: AH5 (SOFTWARE)
51: AH6 (SOFTWARE)
52: AH7 (SOFTWARE)
53: AH8 (SOFTWARE)
54: AH9 (SOFTWARE)
55: AI1 (SOFTWARE)
56: AI2 (SOFTWARE)
57: AI3 (SOFTWARE)
58: AI4 (SOFTWARE)
59: AI5 (SOFTWARE)
60: AI6 (SOFTWARE)
61: AI7 (SOFTWARE)
62: AI8 (SOFTWARE)
63: AI9 (SOFTWARE)
64: AJ1 (SOFTWARE)
65: AJ2 (SOFTWARE)
66: AJ3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:228 , 48Y A:402 , HOH A:563 , ASP B:204 , HOH B:582
binding site for residue MG A 401
02
AC2
SOFTWARE
SER A:72 , ARG A:85 , ARG A:88 , ARG A:98 , ARG A:118 , TYR A:125 , ASP A:228 , MG A:401 , NAI A:403 , HOH A:530 , HOH A:537 , HOH A:541 , HOH A:563 , LYS B:171 , ASN B:173 , VAL B:174 , ASP B:204 , HOH B:582
binding site for residue 48Y A 402
03
AC3
SOFTWARE
ILE A:13 , PHE A:67 , ALA A:69 , ALA A:70 , THR A:71 , SER A:72 , LEU A:241 , GLU A:257 , HIS A:260 , GLY A:261 , SER A:262 , ALA A:263 , ASP A:265 , ILE A:266 , ASN A:273 , 48Y A:402 , HOH A:512 , HOH A:518 , HOH A:526 , HOH A:530 , HOH A:564 , HOH A:566 , HOH A:617 , HOH A:621 , ASN B:173 , ILE B:202 , ASN B:205 , GOL B:403 , HOH B:601
binding site for residue NAI A 403
04
AC4
SOFTWARE
ASP A:204 , ASP B:228 , 48Y B:401 , HOH B:584 , HOH B:585
binding site for residue MG A 404
05
AC5
SOFTWARE
MET A:208 , ARG A:213 , HOH A:615 , GLY B:240 , LEU B:241 , ASP B:313
binding site for residue GOL A 405
06
AC6
SOFTWARE
LEU A:124 , GLN A:179 , THR A:223 , ASN A:224 , LEU A:225
binding site for residue GOL A 406
07
AC7
SOFTWARE
ILE A:157 , ARG A:161
binding site for residue GOL A 407
08
AC8
SOFTWARE
PRO A:99 , LEU A:279 , GLU A:298 , HOH A:612
binding site for residue GOL A 408
09
AC9
SOFTWARE
ARG A:213 , HOH A:592
binding site for residue SO4 A 409
10
AD1
SOFTWARE
ASP A:200 , ILE A:202 , HOH A:501 , HOH A:506 , THR B:74 , LYS D:269
binding site for residue SO4 A 410
11
AD2
SOFTWARE
PRO A:73 , THR A:74 , ARG A:75 , SO4 A:415 , HOH A:619
binding site for residue SO4 A 411
12
AD3
SOFTWARE
TYR A:94 , ALA A:153 , ARG A:156
binding site for residue SO4 A 412
13
AD4
SOFTWARE
ARG A:310
binding site for residue SO4 A 413
14
AD5
SOFTWARE
TYR A:94 , ARG A:152 , ARG A:156 , HOH A:519 , HOH A:534 , HOH A:595 , HOH A:596
binding site for residue SO4 A 414
15
AD6
SOFTWARE
TRP A:41 , THR A:71 , SO4 A:411 , HOH A:619
binding site for residue SO4 A 415
16
AD7
SOFTWARE
LYS A:171 , ASN A:173 , VAL A:174 , ASP A:204 , MG A:404 , SER B:72 , ARG B:85 , ARG B:88 , ARG B:98 , ARG B:118 , TYR B:125 , ASP B:228 , NAI B:402 , HOH B:556 , HOH B:584 , HOH B:598
binding site for residue 48Y B 401
17
AD8
SOFTWARE
ASN A:173 , ILE A:202 , ASN A:205 , HOH A:615 , ILE B:13 , PHE B:67 , ALA B:70 , THR B:71 , SER B:72 , ILE B:84 , LEU B:241 , GLU B:257 , VAL B:259 , HIS B:260 , GLY B:261 , SER B:262 , ALA B:263 , PRO B:264 , ASP B:265 , ILE B:266 , ASN B:273 , 48Y B:401 , HOH B:530 , HOH B:531 , HOH B:534 , HOH B:549 , HOH B:559 , HOH B:586 , HOH B:600 , HOH B:611 , HOH B:620
binding site for residue NAI B 402
18
AD9
SOFTWARE
GLY A:240 , LEU A:241 , ASP A:313 , NAI A:403 , MET B:208 , ARG B:213 , HOH B:601
binding site for residue GOL B 403
19
AE1
SOFTWARE
GLY B:123 , LEU B:124 , GLN B:179 , THR B:223 , LEU B:225
binding site for residue GOL B 404
20
AE2
SOFTWARE
TYR B:94 , ALA B:153 , ARG B:156 , ILE B:157 , GOL B:408 , HOH B:647
binding site for residue GOL B 405
21
AE3
SOFTWARE
PRO B:99 , ARG B:103
binding site for residue GOL B 406
22
AE4
SOFTWARE
ARG B:161 , GOL B:408
binding site for residue GOL B 407
23
AE5
SOFTWARE
MET B:283 , ASP B:286 , GOL B:405 , GOL B:407
binding site for residue GOL B 408
24
AE6
SOFTWARE
ARG B:213 , ARG B:216
binding site for residue SO4 B 409
25
AE7
SOFTWARE
HIS B:167 , GLN B:209 , ARG B:216 , PHE B:217
binding site for residue SO4 B 410
26
AE8
SOFTWARE
ARG B:310
binding site for residue SO4 B 411
27
AE9
SOFTWARE
ARG B:163 , THR B:165 , HOH B:645
binding site for residue SO4 B 412
28
AF1
SOFTWARE
THR A:74 , ASP B:200
binding site for residue SO4 B 413
29
AF2
SOFTWARE
THR B:49 , VAL B:51 , PRO B:52 , GLU B:53 , PHE B:81 , TYR B:86
binding site for residue SO4 B 414
30
AF3
SOFTWARE
PRO B:309 , ARG B:310 , GLY B:316 , ASP B:317
binding site for residue SO4 B 415
31
AF4
SOFTWARE
ARG B:4
binding site for residue SO4 B 416
32
AF5
SOFTWARE
ASP C:228 , 48Y C:402 , HOH C:559 , HOH C:593 , ASP D:204
binding site for residue MG C 401
33
AF6
SOFTWARE
SER C:72 , ARG C:85 , ARG C:88 , ARG C:98 , ARG C:118 , TYR C:125 , ASP C:228 , MG C:401 , NAI C:403 , HOH C:556 , HOH C:559 , HOH C:597 , HOH C:598 , LYS D:171 , ASN D:173 , VAL D:174 , ASP D:204
binding site for residue 48Y C 402
34
AF7
SOFTWARE
ILE C:13 , ALA C:69 , ALA C:70 , THR C:71 , SER C:72 , LEU C:241 , GLU C:257 , VAL C:259 , HIS C:260 , GLY C:261 , SER C:262 , ALA C:263 , ASP C:265 , ILE C:266 , ASN C:273 , 48Y C:402 , HOH C:534 , HOH C:539 , HOH C:543 , HOH C:570 , HOH C:575 , HOH C:580 , HOH C:598 , HOH C:599 , HOH C:610 , ASN D:173 , ILE D:202 , ASN D:205 , MET D:208 , GOL D:403 , HOH D:586 , HOH D:635
binding site for residue NAI C 403
35
AF8
SOFTWARE
ASP C:204 , ASP D:228 , 48Y D:401 , HOH D:573 , HOH D:574
binding site for residue MG C 404
36
AF9
SOFTWARE
MET C:208 , MET C:212 , ARG C:213 , HOH C:517 , GLY D:240 , LEU D:241 , ASP D:313 , NAI D:402
binding site for residue GOL C 405
37
AG1
SOFTWARE
GLY C:10 , HIS C:15 , GLU C:38 , GLU C:42 , THR C:43 , ARG C:46 , HOH C:587
binding site for residue GOL C 406
38
AG2
SOFTWARE
GLY C:123 , LEU C:124 , LEU C:175 , GLN C:179 , THR C:223 , ASN C:224 , LEU C:225
binding site for residue GOL C 407
39
AG3
SOFTWARE
TYR C:94 , ARG C:156
binding site for residue GOL C 408
40
AG4
SOFTWARE
ILE C:249 , MET C:283 , ASP C:286 , GOL C:410
binding site for residue GOL C 409
41
AG5
SOFTWARE
VAL C:115 , ILE C:157 , GOL C:409 , HOH C:648
binding site for residue GOL C 410
42
AG6
SOFTWARE
PRO C:99 , GLU C:298 , GOL C:412 , HOH C:613
binding site for residue GOL C 411
43
AG7
SOFTWARE
PRO C:99 , ALA C:100 , LYS C:101 , ARG C:103 , VAL C:238 , LEU C:243 , PRO C:245 , LEU C:279 , GOL C:411
binding site for residue GOL C 412
44
AG8
SOFTWARE
ARG C:213
binding site for residue SO4 C 413
45
AG9
SOFTWARE
THR C:121 , GLU C:122 , HOH C:578
binding site for residue SO4 C 414
46
AH1
SOFTWARE
ARG C:310
binding site for residue SO4 C 415
47
AH2
SOFTWARE
PRO C:309 , ARG C:310 , GLY C:316 , ASP C:317 , ALA C:318
binding site for residue SO4 C 416
48
AH3
SOFTWARE
PHE C:80 , PHE C:81 , GLY C:82 , ARG C:85 , GLU C:127 , ASN D:173 , VAL D:174 , PRO D:176
binding site for residue SO4 C 417
49
AH4
SOFTWARE
PRO C:52 , GLU C:53 , HOH C:601
binding site for residue SO4 C 418
50
AH5
SOFTWARE
PRO C:73 , THR C:74 , ARG C:75 , SO4 C:421
binding site for residue SO4 C 419
51
AH6
SOFTWARE
ARG C:4 , GLU C:33
binding site for residue SO4 C 420
52
AH7
SOFTWARE
TRP C:41 , SO4 C:419
binding site for residue SO4 C 421
53
AH8
SOFTWARE
LYS B:269 , HOH B:509 , ASP C:200 , THR D:74 , HOH D:541
binding site for residue SO4 C 422
54
AH9
SOFTWARE
LYS C:171 , ASN C:173 , VAL C:174 , ASP C:204 , MG C:404 , SER D:72 , ARG D:85 , ARG D:88 , ARG D:98 , ARG D:118 , TYR D:125 , ASP D:228 , NAI D:402 , HOH D:520 , HOH D:553 , HOH D:573 , HOH D:574
binding site for residue 48Y D 401
55
AI1
SOFTWARE
ASN C:173 , ILE C:202 , ASN C:205 , MET C:208 , GOL C:405 , HOH C:517 , HOH C:595 , ILE D:13 , PHE D:67 , ALA D:70 , THR D:71 , SER D:72 , ILE D:84 , LEU D:241 , GLU D:257 , HIS D:260 , GLY D:261 , SER D:262 , ALA D:263 , ASP D:265 , ILE D:266 , ASN D:273 , 48Y D:401 , HOH D:537 , HOH D:541 , HOH D:566 , HOH D:569 , HOH D:589 , HOH D:590 , HOH D:631
binding site for residue NAI D 402
56
AI2
SOFTWARE
GLY C:240 , LEU C:241 , ASP C:313 , NAI C:403 , MET D:208 , MET D:212 , ARG D:213 , HOH D:568 , HOH D:635
binding site for residue GOL D 403
57
AI3
SOFTWARE
LEU D:124 , GLN D:179 , THR D:223 , ASN D:224 , LEU D:225
binding site for residue GOL D 404
58
AI4
SOFTWARE
TYR D:94 , ARG D:156 , GLY D:250
binding site for residue GOL D 405
59
AI5
SOFTWARE
ASP D:286 , GLU D:298 , GOL D:407
binding site for residue GOL D 406
60
AI6
SOFTWARE
VAL D:97 , ARG D:161 , GOL D:406 , GOL D:408
binding site for residue GOL D 407
61
AI7
SOFTWARE
ILE D:249 , MET D:283 , GOL D:407
binding site for residue GOL D 408
62
AI8
SOFTWARE
ARG D:213 , ARG D:216 , HOH D:608
binding site for residue SO4 D 409
63
AI9
SOFTWARE
HIS D:167 , GLN D:209 , ARG D:216 , PHE D:217
binding site for residue SO4 D 410
64
AJ1
SOFTWARE
PRO D:106 , ARG D:310 , HOH D:633
binding site for residue SO4 D 411
65
AJ2
SOFTWARE
HOH B:608 , ARG D:89 , GLU D:122 , VAL D:141
binding site for residue SO4 D 412
66
AJ3
SOFTWARE
PRO D:309 , ARG D:310 , GLY D:316 , ASP D:317 , HOH D:632
binding site for residue SO4 D 413
[
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