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Biol. Unit 1
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
[
close entry info
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Hetero Components
(5, 32)
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
15
Ligand/Ion
ACETATE ION
2
GOL
13
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
2
Ligand/Ion
UNKNOWN ATOM OR 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: EC1 (SOFTWARE)
36: EC3 (SOFTWARE)
37: EC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:52 , ARG A:68 , ASP A:69 , ASP A:70 , GOL A:628 , HOH A:1158
BINDING SITE FOR RESIDUE ACT A 601
02
AC2
SOFTWARE
LEU A:263 , HOH A:752 , HOH A:761
BINDING SITE FOR RESIDUE ACT A 602
03
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
04
AC4
SOFTWARE
LYS A:316 , HOH A:938 , LYS B:354 , HOH B:837
BINDING SITE FOR RESIDUE ACT A 604
05
AC5
SOFTWARE
TYR A:300 , HOH A:1213 , ASN B:482
BINDING SITE FOR RESIDUE ACT A 605
06
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
07
AC7
SOFTWARE
GLN A:26 , MET A:27 , L2M A:629 , HOH A:776 , HOH A:787 , HOH A:1187
BINDING SITE FOR RESIDUE ACT A 607
08
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
09
AC9
SOFTWARE
GLU A:210 , THR A:228 , ARG A:231 , HOH A:869 , HOH A:1190 , HOH A:1192 , HOH A:1217
BINDING SITE FOR RESIDUE ACT A 609
10
BC1
SOFTWARE
LYS A:330 , ASP A:331 , ARG A:365 , LYS B:148
BINDING SITE FOR RESIDUE ACT A 610
11
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
12
BC3
SOFTWARE
PRO A:429 , LEU A:430 , LYS A:433
BINDING SITE FOR RESIDUE ACT A 612
13
BC4
SOFTWARE
SER A:53 , TRP A:54 , HOH A:1106 , HOH A:1153 , HOH A:1201 , HOH A:1227
BINDING SITE FOR RESIDUE ACT A 613
14
BC5
SOFTWARE
ASN A:235 , ALA A:237 , TYR A:238 , PHE A:419 , GLN A:423 , HOH A:835 , HOH A:1146
BINDING SITE FOR RESIDUE ACT A 614
15
BC6
SOFTWARE
ASP A:453 , HOH A:898 , HOH A:1098
BINDING SITE FOR RESIDUE ACT A 615
16
BC7
SOFTWARE
LYS A:148 , ASN A:149 , LYS A:157
BINDING SITE FOR RESIDUE GOL A 616
17
BC8
SOFTWARE
ARG A:89 , LEU A:92 , ARG A:95 , VAL A:108 , ASP A:109 , VAL A:110 , ASN A:281 , HOH A:971
BINDING SITE FOR RESIDUE GOL A 617
18
BC9
SOFTWARE
SER A:31 , MET A:32 , LYS A:39 , GLU A:491 , ILE A:492 , GLU A:495 , HOH A:716 , HOH A:857 , HOH A:970 , HOH A:1177
BINDING SITE FOR RESIDUE GOL A 618
19
CC1
SOFTWARE
ASN A:220 , GLU A:221 , GLY A:222 , ASP A:350 , LEU A:352 , SER A:353 , HOH A:977 , HOH A:981 , HOH A:1178 , HOH A:1205
BINDING SITE FOR RESIDUE GOL A 619
20
CC2
SOFTWARE
PRO A:11 , GLY A:219 , ASN A:220 , GLY A:222 , LEU A:223 , GOL A:626 , HOH A:1205
BINDING SITE FOR RESIDUE GOL A 620
21
CC3
SOFTWARE
ASP A:427 , ARG A:457
BINDING SITE FOR RESIDUE GOL A 621
22
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
23
CC5
SOFTWARE
ALA A:99 , ARG A:231 , GLN A:234 , TYR A:284 , VAL A:413 , HOH A:1087 , HOH A:1105
BINDING SITE FOR RESIDUE GOL A 623
24
CC6
SOFTWARE
ASP A:109 , THR A:121 , LYS A:354 , GLU A:358 , GOL A:627 , HOH A:1083 , HOH A:1136 , HOH A:1194
BINDING SITE FOR RESIDUE GOL A 624
25
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
26
CC8
SOFTWARE
TRP A:10 , MET A:472 , ALA A:489 , THR A:490 , GOL A:620 , HOH A:922 , HOH A:924 , HOH A:1040
BINDING SITE FOR RESIDUE GOL A 626
27
CC9
SOFTWARE
LYS A:354 , GOL A:624 , HOH A:1083 , HOH A:1230 , HIS B:150
BINDING SITE FOR RESIDUE GOL A 627
28
DC1
SOFTWARE
ARG A:68 , ACT A:601 , HOH A:1231
BINDING SITE FOR RESIDUE GOL A 628
29
DC2
SOFTWARE
TYR A:22 , THR A:23 , MET A:27 , TRP A:100 , ARG A:137 , TRP A:398 , TYR A:402 , HIS A:416 , ACT A:607 , HOH A:776 , HOH A:919 , HOH A:1195
BINDING SITE FOR RESIDUE L2M A 629
30
DC3
SOFTWARE
THR A:441 , HIS A:442 , ASP A:443 , HOH A:1188
BINDING SITE FOR RESIDUE SO4 A 632
31
DC4
SOFTWARE
GLU A:187 , TRP B:54
BINDING SITE FOR RESIDUE ACT B 601
32
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
33
DC7
SOFTWARE
LYS A:335 , HOH A:1209 , ARG B:341 , HOH B:1092
BINDING SITE FOR RESIDUE ACT B 604
34
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
35
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
36
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
37
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:
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
-
[
close PROSITE info
]
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_d4dcya_ (A:)
1b: SCOP_d4dcyb_ (B:)
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Classes
(
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(
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Superfamilies
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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
d4dcya_
A:
1b
d4dcyb_
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
(0, 0)
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all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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