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4DCX
Biol. Unit 1
Info
Asym.Unit (366 KB)
Biol.Unit 1 (183 KB)
Biol.Unit 2 (179 KB)
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Title
:
X-RAY STRUCTURE OF NIKA IN COMPLEX WITH FE(1R,2R)-N,N'-BIS(2-PYRIDYLMETHYL)-N,N'-DICARBOXYMETHYL-1,2-CYCLOHEXANEDIAMINE
Authors
:
M. V. Cherrier, E. Girgenti, P. Amara, M. Iannello, C. Marchi-Delapier J. C. Fontecilla-Camps, S. Menage, C. Cavazza
Date
:
18 Jan 12 (Deposition) - 09 May 12 (Release) - 13 Jun 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Transport Protein, Protein-Bound Iron Complex, Metal Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. V. Cherrier, E. Girgenti, P. Amara, M. Iannello, C. Marchi-Delapierre, J. C. Fontecilla-Camps, S. Menage, C. Cavazza
The Structure Of The Periplasmic Nickel-Binding Protein Nik Provides Insights For Artificial Metalloenzyme Design.
J. Biol. Inorg. Chem. V. 17 817 2012
[
close entry info
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Hetero Components
(4, 30)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1aa: ACETATE ION (ACTaa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
1h: ACETATE ION (ACTh)
1i: ACETATE ION (ACTi)
1j: ACETATE ION (ACTj)
1k: ACETATE ION (ACTk)
1l: ACETATE ION (ACTl)
1m: ACETATE ION (ACTm)
1n: ACETATE ION (ACTn)
1o: ACETATE ION (ACTo)
1p: ACETATE ION (ACTp)
1q: ACETATE ION (ACTq)
1r: ACETATE ION (ACTr)
1s: ACETATE ION (ACTs)
1t: ACETATE ION (ACTt)
1u: ACETATE ION (ACTu)
1v: ACETATE ION (ACTv)
1w: ACETATE ION (ACTw)
1x: ACETATE ION (ACTx)
1y: ACETATE ION (ACTy)
1z: ACETATE ION (ACTz)
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)
3a: {2,2'-[(1R,2R)-CYCLOHEXANE-1,2-DIY... (L2Da)
3b: {2,2'-[(1R,2R)-CYCLOHEXANE-1,2-DIY... (L2Db)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
17
Ligand/Ion
ACETATE ION
2
GOL
10
Ligand/Ion
GLYCEROL
3
L2D
1
Ligand/Ion
{2,2'-[(1R,2R)-CYCLOHEXANE-1,2-DIYLBIS{[(PYRIDIN-2-YL-KAPPAN)METHYL]IMINO-KAPPAN}]DIACETATO-KAPPAO(2-)}IRON
4
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(37, 37)
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: DC6 (SOFTWARE)
33: DC7 (SOFTWARE)
34: DC8 (SOFTWARE)
35: EC4 (SOFTWARE)
36: FC1 (SOFTWARE)
37: FC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:441 , HIS A:442 , ASP A:443 , HOH A:1013
BINDING SITE FOR RESIDUE SO4 A 601
02
AC2
SOFTWARE
ASN A:261 , GLU A:262 , LEU A:263 , HOH A:744 , HOH A:755
BINDING SITE FOR RESIDUE SO4 A 602
03
AC3
SOFTWARE
GLU A:187 , HOH A:1182 , TRP B:54
BINDING SITE FOR RESIDUE ACT A 603
04
AC4
SOFTWARE
SER A:53 , TRP A:54 , HOH A:791
BINDING SITE FOR RESIDUE ACT A 604
05
AC5
SOFTWARE
PRO A:327 , ALA A:328 , ACT A:615 , HOH A:1211 , ARG B:365
BINDING SITE FOR RESIDUE ACT A 605
06
AC6
SOFTWARE
GLN A:361 , SER A:372 , LEU A:373 , HOH A:977 , LYS B:157 , HOH B:864 , HOH B:944
BINDING SITE FOR RESIDUE ACT A 606
07
AC7
SOFTWARE
LEU A:430 , LYS A:433 , HOH A:819 , HOH A:957
BINDING SITE FOR RESIDUE ACT A 607
08
AC8
SOFTWARE
LYS A:316 , HOH A:1126
BINDING SITE FOR RESIDUE ACT A 608
09
AC9
SOFTWARE
ARG A:457
BINDING SITE FOR RESIDUE ACT A 609
10
BC1
SOFTWARE
ASN A:149 , LYS A:157 , HOH A:1183
BINDING SITE FOR RESIDUE ACT A 610
11
BC2
SOFTWARE
HOH A:1192
BINDING SITE FOR RESIDUE ACT A 611
12
BC3
SOFTWARE
GLN A:168 , LYS A:193 , LYS B:477
BINDING SITE FOR RESIDUE ACT A 612
13
BC4
SOFTWARE
ARG A:68 , HOH A:1207
BINDING SITE FOR RESIDUE ACT A 613
14
BC5
SOFTWARE
SER A:243 , GLN A:244 , TYR A:485 , HOH A:874 , HOH A:893 , HOH A:896 , HOH A:1019
BINDING SITE FOR RESIDUE ACT A 614
15
BC6
SOFTWARE
ALA A:328 , ACT A:605 , HOH A:1012 , ALA B:362 , ARG B:365 , GLN B:366
BINDING SITE FOR RESIDUE ACT A 615
16
BC7
SOFTWARE
ARG A:386 , HOH A:917 , ASP B:460 , HOH B:758
BINDING SITE FOR RESIDUE ACT A 616
17
BC8
SOFTWARE
LYS A:52 , ARG A:68 , ASP A:69 , ASP A:70
BINDING SITE FOR RESIDUE ACT A 617
18
BC9
SOFTWARE
ASN A:235 , ALA A:237 , TYR A:238 , PHE A:419 , GLN A:423 , HOH A:827 , HOH A:1133
BINDING SITE FOR RESIDUE ACT A 618
19
CC1
SOFTWARE
LYS A:123 , HOH A:866 , HOH A:930 , HOH A:955 , HOH A:1004 , HOH A:1140 , HOH A:1162
BINDING SITE FOR RESIDUE ACT A 619
20
CC2
SOFTWARE
GLY A:219 , ASN A:220 , GLY A:222 , LEU A:223 , GOL A:623 , HOH A:1124 , HOH A:1125
BINDING SITE FOR RESIDUE GOL A 620
21
CC3
SOFTWARE
ARG A:89 , LEU A:92 , ARG A:95 , VAL A:108 , ASP A:109 , VAL A:110 , ASN A:281 , GOL A:626 , HOH A:914 , HOH A:1076
BINDING SITE FOR RESIDUE GOL A 621
22
CC4
SOFTWARE
LYS A:330 , ASP A:331 , ILE A:332 , ARG A:365
BINDING SITE FOR RESIDUE GOL A 622
23
CC5
SOFTWARE
ASN A:220 , GLU A:247 , ARG A:396 , MET A:472 , ALA A:489 , GOL A:620 , HOH A:876 , HOH A:909 , HOH A:1061
BINDING SITE FOR RESIDUE GOL A 623
24
CC6
SOFTWARE
LYS A:316 , HOH A:885 , HOH A:1017 , HOH A:1047 , HOH A:1197
BINDING SITE FOR RESIDUE GOL A 624
25
CC7
SOFTWARE
VAL A:273 , ASN A:274 , LYS A:275 , LYS A:276 , SER A:308 , GLN A:309 , TYR A:310 , HOH A:875 , HOH A:988 , HOH A:1001
BINDING SITE FOR RESIDUE GOL A 625
26
CC8
SOFTWARE
ARG A:89 , ILE A:359 , ALA A:362 , ASP A:363 , GOL A:621 , HOH A:882 , HOH A:901 , HOH A:918 , HOH A:974 , HOH A:1152
BINDING SITE FOR RESIDUE GOL A 626
27
CC9
SOFTWARE
SER A:31 , ARG A:140 , GLU A:491 , ILE A:492 , GLU A:495 , HOH A:714 , HOH A:1050 , HOH A:1180 , HOH A:1210
BINDING SITE FOR RESIDUE GOL A 627
28
DC1
SOFTWARE
TYR A:382 , GLN A:385 , SER A:415 , HIS A:416 , L2D A:630 , HOH A:1159
BINDING SITE FOR RESIDUE GOL A 628
29
DC2
SOFTWARE
GLY A:44 , GLN A:131 , PRO A:299 , TYR A:300
BINDING SITE FOR RESIDUE GOL A 629
30
DC3
SOFTWARE
TYR A:22 , THR A:23 , MET A:27 , TRP A:100 , ARG A:137 , TRP A:398 , HIS A:416 , THR A:490 , GOL A:628 , HOH A:873 , HOH A:1159 , SO4 B:601
BINDING SITE FOR RESIDUE L2D A 630
31
DC4
SOFTWARE
THR A:23 , PRO A:24 , GLN A:26 , L2D A:630 , HOH A:769 , LYS B:321
BINDING SITE FOR RESIDUE SO4 B 601
32
DC6
SOFTWARE
LYS A:354 , HIS B:150 , HOH B:1045
BINDING SITE FOR RESIDUE ACT B 603
33
DC7
SOFTWARE
ARG A:389 , ASP B:427 , LEU B:430 , HOH B:931 , HOH B:996
BINDING SITE FOR RESIDUE ACT B 604
34
DC8
SOFTWARE
LYS A:335 , ARG B:341 , HOH B:945 , HOH B:1008
BINDING SITE FOR RESIDUE ACT B 605
35
EC4
SOFTWARE
ASN A:75 , GLY A:76 , THR B:203 , PRO B:225 , ASP B:227 , THR B:228 , HOH B:774
BINDING SITE FOR RESIDUE ACT B 610
36
FC1
SOFTWARE
GLU A:182 , ASN B:235 , TYR B:238 , HOH B:904 , HOH B:941
BINDING SITE FOR RESIDUE GOL B 616
37
FC3
SOFTWARE
GLU A:334 , LYS A:335 , ASN A:336 , GLY A:337 , HOH A:1138 , HOH A:1175 , ACT B:606 , HOH B:854
BINDING SITE FOR RESIDUE GOL B 618
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: SBP_BACTERIAL_5 (A:51-73)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SBP_BACTERIAL_5
PS01040
Bacterial extracellular solute-binding proteins, family 5 signature.
NIKA_ECOLI
73-95
1
A:51-73
-
[
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]
Exons
(0, 0)
Info
All Exons
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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, 2)
Info
All SCOP Domains
1a: SCOP_d4dcxa_ (A:)
1b: SCOP_d4dcxb_ (B:)
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Classes
(
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(
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(
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Superfamilies
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(
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Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Periplasmic binding protein-like II
(813)
Superfamily
:
Periplasmic binding protein-like II
(813)
Family
:
Phosphate binding protein-like
(463)
Protein domain
:
Nickel-binding periplasmic protein NikA
(18)
Escherichia coli [TaxId: 562]
(18)
1a
d4dcxa_
A:
1b
d4dcxb_
B:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
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all PFAM domains
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Sorry, no Info available
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