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4DCY
Biol. Unit 2
Info
Asym.Unit (368 KB)
Biol.Unit 1 (183 KB)
Biol.Unit 2 (182 KB)
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(1)
Title
:
X-RAY STRUCTURE OF NIKA IN COMPLEX WITH FE(1S,2S)-N,N-KAPPA-BIS(2-PYRIDYLMETHYL)-N-CARBOXYMETHYL-N-KAPPA-METHYL-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, 12)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
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)
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: {(R)-N-[(1S,2S)-2-{METHYL[(PYRIDIN... (L2Ma)
3b: {(R)-N-[(1S,2S)-2-{METHYL[(PYRIDIN... (L2Mb)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
5a: UNKNOWN ATOM OR ION (UNXa)
5b: UNKNOWN ATOM OR ION (UNXb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
5
Ligand/Ion
ACETATE ION
2
GOL
5
Ligand/Ion
GLYCEROL
3
L2M
1
Ligand/Ion
{(R)-N-[(1S,2S)-2-{METHYL[(PYRIDIN-2-YL-KAPPAN)METHYL]AMINO-KAPPAN}CYCLOHEXYL]-N-[(PYRIDIN-2-YL-KAPPAN)METHYL]GLYCINATO-KAPPA~2~N,O}IRON(2+)
4
SO4
1
Ligand/Ion
SULFATE ION
5
UNX
-1
Ligand/Ion
UNKNOWN ATOM OR ION
[
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Sites
(22, 22)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC8 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: CC4 (SOFTWARE)
09: CC7 (SOFTWARE)
10: CC9 (SOFTWARE)
11: DC4 (SOFTWARE)
12: DC5 (SOFTWARE)
13: DC6 (SOFTWARE)
14: DC7 (SOFTWARE)
15: DC8 (SOFTWARE)
16: DC9 (SOFTWARE)
17: EC1 (SOFTWARE)
18: EC2 (SOFTWARE)
19: EC3 (SOFTWARE)
20: EC4 (SOFTWARE)
21: EC5 (SOFTWARE)
22: EC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
SER A:243 , GLN A:244 , PRO A:245 , GLN A:288 , HOH A:860 , HOH A:948 , HOH A:1075 , HOH A:1086 , GLN B:288 , SER B:297 , HOH B:857
BINDING SITE FOR RESIDUE ACT A 603
02
AC4
SOFTWARE
LYS A:316 , HOH A:938 , LYS B:354 , HOH B:837
BINDING SITE FOR RESIDUE ACT A 604
03
AC5
SOFTWARE
TYR A:300 , HOH A:1213 , ASN B:482
BINDING SITE FOR RESIDUE ACT A 605
04
AC6
SOFTWARE
PRO A:245 , GLN A:288 , ALA A:295 , SER A:297 , TYR A:469 , HOH A:759 , HOH A:1130 , GLN B:244 , HOH B:953
BINDING SITE FOR RESIDUE ACT A 606
05
AC8
SOFTWARE
LYS A:335 , ASN A:336 , GLY A:337 , HOH A:1181 , GOL B:607 , HOH B:911 , HOH B:1096
BINDING SITE FOR RESIDUE ACT A 608
06
BC1
SOFTWARE
LYS A:330 , ASP A:331 , ARG A:365 , LYS B:148
BINDING SITE FOR RESIDUE ACT A 610
07
BC2
SOFTWARE
GLN A:361 , LEU A:373 , HOH A:1004 , HOH A:1099 , HOH A:1117 , HOH A:1160 , HOH A:1196 , HOH B:821
BINDING SITE FOR RESIDUE ACT A 611
08
CC4
SOFTWARE
ASN A:75 , GLY A:76 , HOH A:1222 , THR B:203 , PRO B:225 , ASP B:227 , ACT B:603 , HOH B:1063
BINDING SITE FOR RESIDUE GOL A 622
09
CC7
SOFTWARE
TYR A:22 , THR A:23 , ARG A:97 , HOH A:1214 , TYR B:271 , LYS B:306 , LYS B:314
BINDING SITE FOR RESIDUE GOL A 625
10
CC9
SOFTWARE
LYS A:354 , GOL A:624 , HOH A:1083 , HOH A:1230 , HIS B:150
BINDING SITE FOR RESIDUE GOL A 627
11
DC4
SOFTWARE
GLU A:187 , TRP B:54
BINDING SITE FOR RESIDUE ACT B 601
12
DC5
SOFTWARE
LYS B:52 , ARG B:68 , ASP B:69 , ASP B:70
BINDING SITE FOR RESIDUE ACT B 602
13
DC6
SOFTWARE
GOL A:622 , PRO B:225 , LEU B:352 , HOH B:820 , HOH B:968 , HOH B:1063 , HOH B:1131
BINDING SITE FOR RESIDUE ACT B 603
14
DC7
SOFTWARE
LYS A:335 , HOH A:1209 , ARG B:341 , HOH B:1092
BINDING SITE FOR RESIDUE ACT B 604
15
DC8
SOFTWARE
ARG A:386 , THR B:456 , ASP B:460 , HOH B:939 , HOH B:1002 , HOH B:1013
BINDING SITE FOR RESIDUE ACT B 605
16
DC9
SOFTWARE
TRP B:10 , PRO B:11 , ARG B:205 , GLY B:219 , ASN B:220 , HOH B:969
BINDING SITE FOR RESIDUE GOL B 606
17
EC1
SOFTWARE
ASN A:336 , ACT A:608 , LYS B:330 , ASP B:331 , ILE B:332 , HOH B:1030 , HOH B:1096
BINDING SITE FOR RESIDUE GOL B 607
18
EC2
SOFTWARE
ASN B:274 , LYS B:275 , LYS B:276 , VAL B:289 , SER B:308 , GLN B:309 , TYR B:310 , HOH B:843
BINDING SITE FOR RESIDUE GOL B 608
19
EC3
SOFTWARE
ARG A:384 , ARG A:389 , ASP B:427 , LEU B:430 , ARG B:457 , HOH B:1103
BINDING SITE FOR RESIDUE GOL B 609
20
EC4
SOFTWARE
GLU B:221 , VAL B:249 , SER B:353 , MET B:356 , PHE B:394 , HIS B:395 , ARG B:396 , HOH B:1020
BINDING SITE FOR RESIDUE GOL B 610
21
EC5
SOFTWARE
TYR B:22 , MET B:27 , TRP B:100 , ARG B:137 , TRP B:398 , SER B:410 , HIS B:416 , THR B:490 , HOH B:712 , HOH B:781 , HOH B:1004
BINDING SITE FOR RESIDUE L2M B 611
22
EC6
SOFTWARE
LYS A:321 , ARG B:389 , HOH B:1060
BINDING SITE FOR RESIDUE SO4 B 612
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
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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
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_d4dcya_ (A:)
1b: SCOP_d4dcyb_ (B:)
View:
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Classes
(
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(
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Folds
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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
d4dcya_
A:
1b
d4dcyb_
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
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Sorry, no Info available
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Atom Selection
(currently selected atoms:
all
)
Protein
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Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain B
Asymmetric Unit 1
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