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4DCX
Biol. Unit 2
Info
Asym.Unit (366 KB)
Biol.Unit 1 (183 KB)
Biol.Unit 2 (179 KB)
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(1)
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
[
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Hetero Components
(4, 20)
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
10
Ligand/Ion
ACETATE ION
2
GOL
8
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
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
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Sites
(27, 27)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC5 (SOFTWARE)
03: AC6 (SOFTWARE)
04: BC3 (SOFTWARE)
05: BC6 (SOFTWARE)
06: BC7 (SOFTWARE)
07: DC3 (SOFTWARE)
08: DC4 (SOFTWARE)
09: DC5 (SOFTWARE)
10: DC6 (SOFTWARE)
11: DC7 (SOFTWARE)
12: DC8 (SOFTWARE)
13: DC9 (SOFTWARE)
14: EC1 (SOFTWARE)
15: EC2 (SOFTWARE)
16: EC3 (SOFTWARE)
17: EC4 (SOFTWARE)
18: EC5 (SOFTWARE)
19: EC6 (SOFTWARE)
20: EC7 (SOFTWARE)
21: EC8 (SOFTWARE)
22: EC9 (SOFTWARE)
23: FC1 (SOFTWARE)
24: FC2 (SOFTWARE)
25: FC3 (SOFTWARE)
26: FC4 (SOFTWARE)
27: FC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
GLU A:187 , HOH A:1182 , TRP B:54
BINDING SITE FOR RESIDUE ACT A 603
02
AC5
SOFTWARE
PRO A:327 , ALA A:328 , ACT A:615 , HOH A:1211 , ARG B:365
BINDING SITE FOR RESIDUE ACT A 605
03
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
04
BC3
SOFTWARE
GLN A:168 , LYS A:193 , LYS B:477
BINDING SITE FOR RESIDUE ACT A 612
05
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
06
BC7
SOFTWARE
ARG A:386 , HOH A:917 , ASP B:460 , HOH B:758
BINDING SITE FOR RESIDUE ACT A 616
07
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
08
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
09
DC5
SOFTWARE
ARG B:384 , ARG B:389 , HOH B:857 , HOH B:951
BINDING SITE FOR RESIDUE ACT B 602
10
DC6
SOFTWARE
LYS A:354 , HIS B:150 , HOH B:1045
BINDING SITE FOR RESIDUE ACT B 603
11
DC7
SOFTWARE
ARG A:389 , ASP B:427 , LEU B:430 , HOH B:931 , HOH B:996
BINDING SITE FOR RESIDUE ACT B 604
12
DC8
SOFTWARE
LYS A:335 , ARG B:341 , HOH B:945 , HOH B:1008
BINDING SITE FOR RESIDUE ACT B 605
13
DC9
SOFTWARE
LYS B:330 , ASP B:331 , ILE B:332 , GOL B:618
BINDING SITE FOR RESIDUE ACT B 606
14
EC1
SOFTWARE
LYS B:115 , ALA B:256 , ALA B:258
BINDING SITE FOR RESIDUE ACT B 607
15
EC2
SOFTWARE
ASN B:75 , LYS B:433
BINDING SITE FOR RESIDUE ACT B 608
16
EC3
SOFTWARE
THR B:23 , GLN B:26 , L2D B:620 , HOH B:759 , HOH B:956
BINDING SITE FOR RESIDUE ACT B 609
17
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
18
EC5
SOFTWARE
LYS B:72 , GLY B:76 , PRO B:78 , GLN B:423 , LEU B:425 , LYS B:428 , PRO B:429 , HOH B:754 , HOH B:924
BINDING SITE FOR RESIDUE ACT B 611
19
EC6
SOFTWARE
VAL B:273 , ASN B:274 , LYS B:275 , LYS B:276 , GLN B:309 , TYR B:310 , HOH B:812 , HOH B:999
BINDING SITE FOR RESIDUE GOL B 612
20
EC7
SOFTWARE
GLU B:221 , SER B:353 , MET B:356 , PHE B:394 , HIS B:395 , ARG B:396 , HOH B:902
BINDING SITE FOR RESIDUE GOL B 613
21
EC8
SOFTWARE
TRP B:10 , MET B:472 , ALA B:489 , THR B:490 , GOL B:619 , HOH B:881 , HOH B:906 , HOH B:977
BINDING SITE FOR RESIDUE GOL B 614
22
EC9
SOFTWARE
TRP B:10 , ASN B:25 , GLN B:26 , MET B:27 , PHE B:28 , HOH B:759 , HOH B:859
BINDING SITE FOR RESIDUE GOL B 615
23
FC1
SOFTWARE
GLU A:182 , ASN B:235 , TYR B:238 , HOH B:904 , HOH B:941
BINDING SITE FOR RESIDUE GOL B 616
24
FC2
SOFTWARE
TRP B:63 , ALA B:125 , TYR B:126 , TYR B:127 , HIS B:442
BINDING SITE FOR RESIDUE GOL B 617
25
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
26
FC4
SOFTWARE
PRO B:11 , GLY B:219 , ASN B:220 , GLY B:222 , LEU B:223 , GOL B:614
BINDING SITE FOR RESIDUE GOL B 619
27
FC5
SOFTWARE
TYR B:22 , THR B:23 , MET B:27 , TRP B:100 , ARG B:137 , TRP B:398 , HIS B:416 , THR B:490 , ACT B:609 , HOH B:759 , HOH B:874
BINDING SITE FOR RESIDUE L2D B 620
[
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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 (B: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
-
B:51-73
[
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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.
(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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(
)
(
)
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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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Atom Selection
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Protein
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Sidechain
Hetero
Ligand
Solvent
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain B
Asymmetric Unit 1
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