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1VKM
Biol. Unit 3
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Asym.Unit (318 KB)
Biol.Unit 1 (155 KB)
Biol.Unit 2 (154 KB)
Biol.Unit 3 (300 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AN INDIGOIDINE SYNTHASE A (IDGA)-LIKE PROTEIN (TM1464) FROM THERMOTOGA MARITIMA MSB8 AT 1.90 A RESOLUTION
Authors
:
Joint Center For Structural Genomics (Jcsg)
Date
:
09 Jun 04 (Deposition) - 29 Jun 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Biol. Unit 3: A,B,C,D,E,F (1x)
Keywords
:
Indigoidine Synthase A-Like Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Biosynthetic Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Levin, M. D. Miller, R. Schwarzenbacher, D. Mcmullan, P. Abdubek, E. Ambing, T. Biorac, J. Cambell, J. M. Canaves, H. J. Chiu, A. M. Deacon M. Didonato, M. A. Elsliger, A. Godzik, C. Grittini, S. K. Grzechnik, J. Hale, E. Hampton, G. W. Han, J. Haugen, M. Hornsby, L. Jaroszewski, C. Karlak, H. E. Klock, E. Koesema, A. Kreusch, P. Kuhn, S. A. Lesley, A. Morse, K. Moy, E. Nigoghossian, J. Ouyang, R. Page, K. Quijano, R. Reyes, A. Robb, E. Sims, G. Spraggon, R. C. Stevens, H. Van Den Bedem, J. Velasquez, J. Vincent, X. Wang, B. West, G. Wolf, Q. Xu, O. Zagnitko, K. O. Hodgson, J. Wooley, I. A. Wilson
Crystal Structure Of An Indigoidine Synthase A (Inda)-Like Protein (Tm1464) From Thermotoga Maritima At 1. 90 A Resolution Reveals A New Fold.
Proteins V. 59 864 2005
[
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Hetero Components
(3, 77)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
2e: MANGANESE (II) ION (MNe)
2f: MANGANESE (II) ION (MNf)
2g: MANGANESE (II) ION (MNg)
2h: MANGANESE (II) ION (MNh)
2i: MANGANESE (II) ION (MNi)
2j: MANGANESE (II) ION (MNj)
2k: MANGANESE (II) ION (MNk)
2l: MANGANESE (II) ION (MNl)
2m: MANGANESE (II) ION (MNm)
2n: MANGANESE (II) ION (MNn)
2o: MANGANESE (II) ION (MNo)
2p: MANGANESE (II) ION (MNp)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
3ab: SELENOMETHIONINE (MSEab)
3ac: SELENOMETHIONINE (MSEac)
3ad: SELENOMETHIONINE (MSEad)
3ae: SELENOMETHIONINE (MSEae)
3af: SELENOMETHIONINE (MSEaf)
3ag: SELENOMETHIONINE (MSEag)
3ah: SELENOMETHIONINE (MSEah)
3ai: SELENOMETHIONINE (MSEai)
3aj: SELENOMETHIONINE (MSEaj)
3ak: SELENOMETHIONINE (MSEak)
3al: SELENOMETHIONINE (MSEal)
3am: SELENOMETHIONINE (MSEam)
3an: SELENOMETHIONINE (MSEan)
3ao: SELENOMETHIONINE (MSEao)
3ap: SELENOMETHIONINE (MSEap)
3aq: SELENOMETHIONINE (MSEaq)
3ar: SELENOMETHIONINE (MSEar)
3as: SELENOMETHIONINE (MSEas)
3at: SELENOMETHIONINE (MSEat)
3au: SELENOMETHIONINE (MSEau)
3av: SELENOMETHIONINE (MSEav)
3aw: SELENOMETHIONINE (MSEaw)
3ax: SELENOMETHIONINE (MSEax)
3ay: SELENOMETHIONINE (MSEay)
3az: SELENOMETHIONINE (MSEaz)
3b: SELENOMETHIONINE (MSEb)
3ba: SELENOMETHIONINE (MSEba)
3bb: SELENOMETHIONINE (MSEbb)
3bc: SELENOMETHIONINE (MSEbc)
3bd: SELENOMETHIONINE (MSEbd)
3be: SELENOMETHIONINE (MSEbe)
3bf: SELENOMETHIONINE (MSEbf)
3bg: SELENOMETHIONINE (MSEbg)
3bh: SELENOMETHIONINE (MSEbh)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
3y: SELENOMETHIONINE (MSEy)
3z: SELENOMETHIONINE (MSEz)
4a: UNKNOWN LIGAND (UNLa)
4b: UNKNOWN LIGAND (UNLb)
4c: UNKNOWN LIGAND (UNLc)
4d: UNKNOWN LIGAND (UNLd)
4e: UNKNOWN LIGAND (UNLe)
4f: UNKNOWN LIGAND (UNLf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
11
Ligand/Ion
1,2-ETHANEDIOL
2
MN
-1
Ligand/Ion
MANGANESE (II) ION
3
MSE
60
Mod. Amino Acid
SELENOMETHIONINE
4
UNL
6
Ligand/Ion
UNKNOWN LIGAND
[
close Hetero Component info
]
Sites
(33, 33)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:-4 , HIS A:-2 , GLU C:204 , GLU C:206 , HOH C:612 , HIS E:-5
BINDING SITE FOR RESIDUE MN A 300
02
AC2
SOFTWARE
ASP A:126 , HOH A:602 , HOH A:605 , HOH A:606 , HOH A:611 , HOH C:604
BINDING SITE FOR RESIDUE MN A 400
03
AC3
SOFTWARE
GLU A:204 , GLU A:206 , HOH A:626 , HIS B:-2 , HIS B:-4 , HIS F:-5
BINDING SITE FOR RESIDUE MN B 300
04
AC4
SOFTWARE
HOH A:616 , HOH A:636 , ASP B:126 , HOH B:604 , HOH B:607 , HOH B:609
BINDING SITE FOR RESIDUE MN B 400
05
AC5
SOFTWARE
GLU B:204 , GLU B:206 , HOH B:614 , HIS C:-2 , HIS C:-4 , HIS D:-5
BINDING SITE FOR RESIDUE MN C 300
06
AC6
SOFTWARE
HOH B:613 , ASP C:126 , HOH C:610 , HOH C:614 , HOH C:621 , HOH C:636
BINDING SITE FOR RESIDUE MN C 400
07
AC7
SOFTWARE
HIS C:-5 , HIS D:-2 , HIS D:-4 , GLU E:204 , GLU E:206 , HOH E:618
BINDING SITE FOR RESIDUE MN D 300
08
AC8
SOFTWARE
ASP D:126 , HOH D:603 , HOH D:605 , HOH D:609 , HOH E:604 , HOH E:606
BINDING SITE FOR RESIDUE MN D 400
09
AC9
SOFTWARE
HIS A:-5 , HIS E:-2 , HIS E:-4 , GLU F:204 , GLU F:206 , HOH F:605
BINDING SITE FOR RESIDUE MN E 300
10
BC1
SOFTWARE
ASP E:126 , HOH E:609 , HOH E:611 , HOH E:619 , HOH F:618 , HOH F:623
BINDING SITE FOR RESIDUE MN E 400
11
BC2
SOFTWARE
HIS B:-5 , GLU D:204 , GLU D:206 , HOH D:614 , HIS F:-2 , HIS F:-4
BINDING SITE FOR RESIDUE MN F 300
12
BC3
SOFTWARE
HOH D:606 , HOH D:607 , ASP F:126 , HOH F:601 , HOH F:602 , HOH F:603
BINDING SITE FOR RESIDUE MN F 400
13
BC4
SOFTWARE
GLU C:64 , GLU C:65 , GLU C:68 , HOH C:686 , HOH C:716 , HOH C:722
BINDING SITE FOR RESIDUE MN C 401
14
BC5
SOFTWARE
GLU A:229 , HOH A:808 , HOH A:811 , HOH A:818 , GLU F:220
BINDING SITE FOR RESIDUE MN A 401
15
BC6
SOFTWARE
GLU C:4 , GLU F:229 , GLU F:233 , HOH F:736 , HOH F:745 , HOH F:748 , HOH F:755
BINDING SITE FOR RESIDUE MN F 401
16
BC7
SOFTWARE
HOH D:760 , HOH E:717
BINDING SITE FOR RESIDUE MN E 401
17
BC8
SOFTWARE
GLU A:17 , THR A:19 , LYS A:77 , THR A:96 , VAL A:97 , THR A:114 , GLY A:116 , SER A:128 , ASP A:130 , LYS A:147 , HOH A:603 , HOH A:606 , HOH A:608 , HOH A:610 , HOH A:611 , HOH A:612 , HOH A:644 , HOH A:662 , HOH A:790
BINDING SITE FOR RESIDUE UNL A 600
18
BC9
SOFTWARE
HOH A:616 , GLU B:17 , THR B:19 , LYS B:77 , THR B:96 , VAL B:97 , THR B:114 , GLY B:116 , SER B:128 , ASP B:130 , LYS B:147 , THR B:245 , EDO B:601 , HOH B:605 , HOH B:609 , HOH B:610 , HOH B:625 , HOH B:642 , HOH B:644
BINDING SITE FOR RESIDUE UNL B 600
19
CC1
SOFTWARE
GLU C:17 , THR C:19 , LYS C:77 , THR C:96 , VAL C:97 , THR C:114 , GLY C:116 , SER C:128 , ASP C:130 , LYS C:147 , HOH C:605 , HOH C:614 , HOH C:629 , HOH C:632 , HOH C:636 , HOH C:643 , HOH C:646 , HOH C:654 , HOH C:736
BINDING SITE FOR RESIDUE UNL C 600
20
CC2
SOFTWARE
GLU D:17 , THR D:19 , LYS D:77 , THR D:96 , VAL D:97 , THR D:114 , GLY D:116 , SER D:128 , ASP D:130 , LYS D:147 , THR D:245 , HOH D:608 , HOH D:609 , HOH D:612 , HOH D:621 , HOH D:633 , HOH D:644 , HOH D:659 , HOH D:744 , HOH E:604
BINDING SITE FOR RESIDUE UNL D 600
21
CC3
SOFTWARE
GLU E:17 , THR E:19 , LYS E:77 , THR E:96 , VAL E:97 , THR E:114 , GLY E:116 , SER E:128 , ASP E:130 , LYS E:147 , HOH E:608 , HOH E:611 , HOH E:616 , HOH E:652 , HOH E:678 , HOH E:693 , HOH E:700 , HOH F:618
BINDING SITE FOR RESIDUE UNL E 600
22
CC4
SOFTWARE
HOH D:607 , GLU F:17 , THR F:19 , LYS F:77 , THR F:96 , VAL F:97 , THR F:114 , GLY F:116 , SER F:128 , ASP F:130 , LYS F:147 , HOH F:602 , HOH F:604 , HOH F:608 , HOH F:610 , HOH F:626 , HOH F:644 , HOH F:659
BINDING SITE FOR RESIDUE UNL F 600
23
CC5
SOFTWARE
ARG D:81 , HOH D:624 , HOH D:632 , LEU E:166 , PRO E:187
BINDING SITE FOR RESIDUE EDO D 601
24
CC6
SOFTWARE
HIS C:-2 , HIS C:-5 , HIS D:-2 , HIS D:-5
BINDING SITE FOR RESIDUE EDO C 601
25
CC7
SOFTWARE
GLU B:17 , VAL B:20 , THR B:114 , GLY B:115 , GLY B:116 , LYS B:147 , PHE B:177 , ASN B:264 , UNL B:600 , HOH B:697
BINDING SITE FOR RESIDUE EDO B 601
26
CC8
SOFTWARE
THR E:132 , SER E:135 , HOH E:708 , HOH E:710 , LEU F:162
BINDING SITE FOR RESIDUE EDO E 601
27
CC9
SOFTWARE
PRO B:165 , LEU B:166 , HOH B:627 , HOH B:664 , ARG C:81
BINDING SITE FOR RESIDUE EDO B 602
28
DC1
SOFTWARE
HIS A:-5 , HIS A:-2 , HIS A:-4 , HIS E:-2
BINDING SITE FOR RESIDUE EDO A 601
29
DC2
SOFTWARE
ASP D:76 , VAL D:78 , ILE D:85 , VAL D:86 , HOH D:657 , ARG E:185
BINDING SITE FOR RESIDUE EDO D 602
30
DC3
SOFTWARE
VAL D:127 , MSE E:158 , HOH E:610 , HOH E:637
BINDING SITE FOR RESIDUE EDO E 602
31
DC4
SOFTWARE
LEU E:150 , ASP E:151 , VAL E:152 , GLU E:153 , HOH E:654 , HOH E:696 , HOH E:702
BINDING SITE FOR RESIDUE EDO E 603
32
DC5
SOFTWARE
ARG C:138 , LYS C:203 , HOH C:730 , LYS E:-7
BINDING SITE FOR RESIDUE EDO C 602
33
DC6
SOFTWARE
HIS B:-2 , HIS B:-5 , HOH B:663 , HIS F:-2 , HIS F:-3 , HIS F:-4 , HIS F:-5 , HOH F:704
BINDING SITE FOR RESIDUE EDO B 603
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
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Label:
All Exon Boundaries
View:
Label:
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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1vkma_ (A:)
1b: SCOP_d1vkmb_ (B:)
1c: SCOP_d1vkmc_ (C:)
1d: SCOP_d1vkmd_ (D:)
1e: SCOP_d1vkme_ (E:)
1f: SCOP_d1vkmf_ (F:)
View:
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Classes
(
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(
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(
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(
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(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Indigoidine synthase A-like
(1)
Superfamily
:
Indigoidine synthase A-like
(1)
Family
:
Indigoidine synthase A-like
(1)
Protein domain
:
Hypothetical protein TM1464
(1)
Thermotoga maritima [TaxId: 2336]
(1)
1a
d1vkma_
A:
1b
d1vkmb_
B:
1c
d1vkmc_
C:
1d
d1vkmd_
D:
1e
d1vkme_
E:
1f
d1vkmf_
F:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Indigoidine_A_1vkmF01 (F:2-282)
1b: PFAM_Indigoidine_A_1vkmF02 (F:2-282)
1c: PFAM_Indigoidine_A_1vkmF03 (F:2-282)
1d: PFAM_Indigoidine_A_1vkmF04 (F:2-282)
1e: PFAM_Indigoidine_A_1vkmF05 (F:2-282)
1f: PFAM_Indigoidine_A_1vkmF06 (F:2-282)
View:
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Clans
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(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Indigoidine_A]
(1)
Family
:
Indigoidine_A
(1)
Thermotoga maritima
(1)
1a
Indigoidine_A-1vkmF01
F:2-282
1b
Indigoidine_A-1vkmF02
F:2-282
1c
Indigoidine_A-1vkmF03
F:2-282
1d
Indigoidine_A-1vkmF04
F:2-282
1e
Indigoidine_A-1vkmF05
F:2-282
1f
Indigoidine_A-1vkmF06
F:2-282
[
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