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4I9D
Biol. Unit 2
Info
Asym.Unit (382 KB)
Biol.Unit 1 (190 KB)
Biol.Unit 2 (187 KB)
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(1)
Title
:
X-RAY STRUCTURE OF NIKA IN COMPLEX WITH FE-N,N'-BIS(2-PYRIDYLMETHYL)-N-CARBOXYMETHYL-N'-METHYL
Authors
:
M. V. Cherrier, P. Amara, M. Iannello, C. Cavazza
Date
:
05 Dec 12 (Deposition) - 17 Apr 13 (Release) - 17 Apr 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
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
:
C. Esmieu, M. V. Cherrier, P. Amara, E. Girgenti, C. Marchi-Delapierre, F. Oddon, M. Iannello, A. Jorge-Robin, C. Cavazza, S. Menage
An Artificial Oxygenase Built From Scratch: Substrate Binding Site Identified Using A Docking Approach.
Angew. Chem. Int. Ed. Engl. V. 52 3922 2013
[
close entry info
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Hetero Components
(3, 16)
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)
1u: ACETATE ION (ACTu)
1v: ACETATE ION (ACTv)
1w: ACETATE ION (ACTw)
1x: ACETATE ION (ACTx)
1y: ACETATE ION (ACTy)
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)
2s: GLYCEROL (GOLs)
2t: GLYCEROL (GOLt)
2u: GLYCEROL (GOLu)
3a: {(S)-N-(2-{METHYL[(PYRIDIN-2-YL-KA... (L4Da)
3b: {(S)-N-(2-{METHYL[(PYRIDIN-2-YL-KA... (L4Db)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
7
Ligand/Ion
ACETATE ION
2
GOL
8
Ligand/Ion
GLYCEROL
3
L4D
1
Ligand/Ion
{(S)-N-(2-{METHYL[(PYRIDIN-2-YL-KAPPAN)METHYL]AMINO-KAPPAN}ETHYL)-N-[(PYRIDIN-2-YL-KAPPAN)METHYL]GLYCINATO-KAPPA~2~N,O}IRON(2+)
4
SO4
-1
Ligand/Ion
SULFATE ION
[
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Sites
(24, 24)
Info
All Sites
01: AC8 (SOFTWARE)
02: BC4 (SOFTWARE)
03: CC1 (SOFTWARE)
04: CC6 (SOFTWARE)
05: CC7 (SOFTWARE)
06: CC9 (SOFTWARE)
07: DC1 (SOFTWARE)
08: DC7 (SOFTWARE)
09: DC8 (SOFTWARE)
10: DC9 (SOFTWARE)
11: EC1 (SOFTWARE)
12: EC2 (SOFTWARE)
13: EC3 (SOFTWARE)
14: EC4 (SOFTWARE)
15: EC5 (SOFTWARE)
16: EC6 (SOFTWARE)
17: EC7 (SOFTWARE)
18: EC8 (SOFTWARE)
19: EC9 (SOFTWARE)
20: FC1 (SOFTWARE)
21: FC2 (SOFTWARE)
22: FC3 (SOFTWARE)
23: FC4 (SOFTWARE)
24: FC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC8
SOFTWARE
LYS A:330 , ASP A:331 , ARG A:365 , LYS B:148
BINDING SITE FOR RESIDUE GOL A 608
02
BC4
SOFTWARE
PRO A:327 , ALA A:328 , ARG B:365 , HOH B:1189
BINDING SITE FOR RESIDUE ACT A 613
03
CC1
SOFTWARE
PRO A:296 , ASN A:302 , LEU A:303 , GLY A:304 , HOH A:709 , HOH A:991 , HOH A:1174 , HOH A:1316 , PHE B:229 , SER B:233 , LEU B:242
BINDING SITE FOR RESIDUE GOL A 619
04
CC6
SOFTWARE
THR A:23 , GLN A:26 , L4D A:631 , HOH A:772 , HOH A:1226 , HOH B:1110
BINDING SITE FOR RESIDUE ACT A 624
05
CC7
SOFTWARE
LYS A:316 , HOH A:919 , LYS B:354
BINDING SITE FOR RESIDUE ACT A 625
06
CC9
SOFTWARE
LEU A:167 , GLN A:168 , HOH A:975 , HOH A:1311 , HOH A:1335 , VAL B:207 , THR B:211 , ASP B:213
BINDING SITE FOR RESIDUE ACT A 627
07
DC1
SOFTWARE
LYS A:498 , VAL A:500 , HOH A:1314 , HIS B:56 , TRP B:63 , GOL B:611
BINDING SITE FOR RESIDUE ACT A 628
08
DC7
SOFTWARE
ARG A:386 , HOH A:1273 , HOH A:1304 , HOH A:1339 , GLY B:304 , LEU B:305 , LYS B:306 , THR B:456 , HIS B:459 , ASP B:460 , HOH B:768 , HOH B:1199
BINDING SITE FOR RESIDUE GOL A 634
09
DC8
SOFTWARE
TRP B:10 , PRO B:11 , GLY B:219 , ASN B:220 , GLY B:222 , LEU B:223 , GOL B:606 , HOH B:1098
BINDING SITE FOR RESIDUE GOL B 601
10
DC9
SOFTWARE
VAL B:273 , ASN B:274 , LYS B:275 , LYS B:276 , SER B:308 , GLN B:309 , TYR B:310 , HOH B:844 , HOH B:904 , HOH B:1011 , HOH B:1160
BINDING SITE FOR RESIDUE GOL B 602
11
EC1
SOFTWARE
ARG B:389 , GOL B:616 , HOH B:1207
BINDING SITE FOR RESIDUE ACT B 603
12
EC2
SOFTWARE
GLU B:221 , VAL B:249 , SER B:353 , MET B:356 , PHE B:394 , HIS B:395 , ARG B:396 , HOH B:935 , HOH B:1007 , HOH B:1211
BINDING SITE FOR RESIDUE GOL B 604
13
EC3
SOFTWARE
LYS A:354 , HIS B:150
BINDING SITE FOR RESIDUE ACT B 605
14
EC4
SOFTWARE
ASN B:220 , GLU B:247 , ARG B:396 , ALA B:489 , THR B:490 , GOL B:601 , HOH B:965 , HOH B:979 , HOH B:1019
BINDING SITE FOR RESIDUE GOL B 606
15
EC5
SOFTWARE
ARG A:384 , ARG A:389 , ASP B:427 , ARG B:457 , HOH B:954
BINDING SITE FOR RESIDUE ACT B 607
16
EC6
SOFTWARE
LYS A:335 , ARG B:341 , HOH B:1109 , HOH B:1134
BINDING SITE FOR RESIDUE ACT B 608
17
EC7
SOFTWARE
ARG A:97 , HOH A:1014 , HOH A:1276 , LYS B:306 , LYS B:314 , HOH B:991 , HOH B:1035 , HOH B:1173
BINDING SITE FOR RESIDUE ACT B 609
18
EC8
SOFTWARE
ASP B:4 , GLU B:5
BINDING SITE FOR RESIDUE GOL B 610
19
EC9
SOFTWARE
VAL A:500 , ACT A:628 , TRP B:63 , ALA B:125 , TYR B:126 , TYR B:127 , HOH B:880
BINDING SITE FOR RESIDUE GOL B 611
20
FC1
SOFTWARE
THR B:23 , PRO B:24 , GLN B:26 , HOH B:1051
BINDING SITE FOR RESIDUE ACT B 612
21
FC2
SOFTWARE
TYR B:22 , THR B:23 , MET B:27 , TRP B:100 , ARG B:137 , TRP B:398 , THR B:490 , ACT B:615 , HOH B:950 , HOH B:1183 , HOH B:1230 , HOH B:1231 , HOH B:1232
BINDING SITE FOR RESIDUE L4D B 613
22
FC3
SOFTWARE
GLU A:187 , LYS B:52 , SER B:53 , TRP B:54 , HOH B:1107
BINDING SITE FOR RESIDUE GOL B 614
23
FC4
SOFTWARE
GLN B:385 , HIS B:416 , ALA B:417 , L4D B:613 , HOH B:1135
BINDING SITE FOR RESIDUE ACT B 615
24
FC5
SOFTWARE
LYS B:257 , GLU B:343 , SER B:345 , ARG B:384 , ARG B:389 , PHE B:390 , GLY B:391 , ACT B:603 , HOH B:977 , HOH B:1208
BINDING SITE FOR RESIDUE GOL B 616
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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
(, 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
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All Exon Boundaries
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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_d4i9da_ (A:)
1b: SCOP_d4i9db_ (B:)
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Classes
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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
d4i9da_
A:
1b
d4i9db_
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
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Protein
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Sidechain
Hetero
Ligand
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain B
Asymmetric Unit 1
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