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4I9D
Asym. Unit
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
(4, 50)
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
25
Ligand/Ion
ACETATE ION
2
GOL
21
Ligand/Ion
GLYCEROL
3
L4D
2
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
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
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Sites
(50, 50)
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: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:52 , ARG A:68 , ASP A:69 , ASP A:70 , HOH A:1283
BINDING SITE FOR RESIDUE ACT A 601
02
AC2
SOFTWARE
ASN A:261 , LEU A:263 , HOH A:757
BINDING SITE FOR RESIDUE ACT A 602
03
AC3
SOFTWARE
GLY A:219 , ASN A:220 , GLY A:222 , GOL A:610 , HOH A:881 , HOH A:1348
BINDING SITE FOR RESIDUE GOL A 603
04
AC4
SOFTWARE
THR A:441 , HIS A:442 , ASP A:443 , HOH A:1171
BINDING SITE FOR RESIDUE SO4 A 604
05
AC5
SOFTWARE
PHE A:147 , LYS A:148 , ASN A:149 , LYS A:157 , HOH A:884
BINDING SITE FOR RESIDUE SO4 A 605
06
AC6
SOFTWARE
ARG A:89 , LEU A:92 , ARG A:95 , ILE A:107 , VAL A:108 , ASP A:109 , VAL A:110 , ASN A:281 , HOH A:943 , HOH A:946
BINDING SITE FOR RESIDUE GOL A 606
07
AC7
SOFTWARE
SER A:53 , TRP A:54 , HOH A:797 , HOH A:1292
BINDING SITE FOR RESIDUE ACT A 607
08
AC8
SOFTWARE
LYS A:330 , ASP A:331 , ARG A:365 , LYS B:148
BINDING SITE FOR RESIDUE GOL A 608
09
AC9
SOFTWARE
ARG A:180 , LYS A:188 , LYS A:192
BINDING SITE FOR RESIDUE GOL A 609
10
BC1
SOFTWARE
ASN A:220 , GLU A:247 , ARG A:396 , MET A:472 , ALA A:489 , THR A:490 , GOL A:603 , L4D A:631 , HOH A:906 , HOH A:955 , HOH A:1291
BINDING SITE FOR RESIDUE GOL A 610
11
BC2
SOFTWARE
LYS A:123 , THR A:203 , GOL A:633 , HOH A:895 , HOH A:981 , HOH A:986 , HOH A:1067 , HOH A:1102 , HOH A:1219
BINDING SITE FOR RESIDUE ACT A 611
12
BC3
SOFTWARE
GLU A:221 , GLY A:222 , ASP A:350 , SER A:353 , ARG A:396 , HOH A:952 , HOH A:976 , HOH A:1001 , HOH A:1348
BINDING SITE FOR RESIDUE GOL A 612
13
BC4
SOFTWARE
PRO A:327 , ALA A:328 , ARG B:365 , HOH B:1189
BINDING SITE FOR RESIDUE ACT A 613
14
BC5
SOFTWARE
VAL A:273 , ASN A:274 , LYS A:275 , LYS A:276 , ASP A:291 , SER A:308 , GLN A:309 , TYR A:310 , HOH A:904 , HOH A:1089 , HOH A:1150 , HOH A:1192 , HOH A:1253 , HOH A:1282
BINDING SITE FOR RESIDUE GOL A 614
15
BC6
SOFTWARE
GLN A:361 , SER A:372 , LEU A:373 , HOH A:1026 , HOH A:1059
BINDING SITE FOR RESIDUE ACT A 615
16
BC7
SOFTWARE
LEU A:430 , LYS A:433 , HOH A:828 , HOH A:1024 , HOH A:1333
BINDING SITE FOR RESIDUE ACT A 616
17
BC8
SOFTWARE
GLN A:313 , LYS A:316 , HOH A:1187 , HOH A:1298
BINDING SITE FOR RESIDUE ACT A 617
18
BC9
SOFTWARE
ARG A:457 , HOH A:1204
BINDING SITE FOR RESIDUE ACT A 618
19
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
20
CC2
SOFTWARE
ASP A:453 , HOH A:856 , HOH A:1160
BINDING SITE FOR RESIDUE ACT A 620
21
CC3
SOFTWARE
GLN A:174 , ASN A:197 , VAL A:198 , HOH A:1025 , HOH A:1297
BINDING SITE FOR RESIDUE ACT A 621
22
CC4
SOFTWARE
SER A:31 , MET A:32 , LYS A:39 , ALA A:486 , GLU A:491 , ILE A:492 , PRO A:493 , GLU A:495 , HOH A:715 , HOH A:851 , HOH A:1279
BINDING SITE FOR RESIDUE GOL A 622
23
CC5
SOFTWARE
TYR A:271 , LYS A:306 , LYS A:314 , HOH A:753 , HOH A:1207
BINDING SITE FOR RESIDUE ACT A 623
24
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
25
CC7
SOFTWARE
LYS A:316 , HOH A:919 , LYS B:354
BINDING SITE FOR RESIDUE ACT A 625
26
CC8
SOFTWARE
GLU A:86 , ARG A:89 , PRO A:144 , PHE A:147 , HIS A:150 , HOH A:1017
BINDING SITE FOR RESIDUE GOL A 626
27
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
28
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
29
DC2
SOFTWARE
GLU A:479 , PRO A:499 , VAL A:500 , HOH A:1359
BINDING SITE FOR RESIDUE ACT A 629
30
DC3
SOFTWARE
ARG A:68 , HOH A:1030
BINDING SITE FOR RESIDUE ACT A 630
31
DC4
SOFTWARE
TYR A:22 , THR A:23 , MET A:27 , TRP A:100 , ARG A:137 , TRP A:398 , THR A:490 , GOL A:610 , ACT A:624 , HOH A:902 , HOH A:1226 , HOH A:1362 , HOH A:1363 , HOH A:1364 , HOH A:1365
BINDING SITE FOR RESIDUE L4D A 631
32
DC5
SOFTWARE
ASN A:235 , ALA A:237 , PHE A:419 , GLN A:423 , PRO A:429 , HOH A:835 , HOH A:1289
BINDING SITE FOR RESIDUE GOL A 632
33
DC6
SOFTWARE
ASN A:105 , ASP A:227 , THR A:228 , ARG A:231 , ACT A:611 , HOH A:1022 , HOH A:1087 , HOH A:1208 , HOH A:1296
BINDING SITE FOR RESIDUE GOL A 633
34
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
35
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
36
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
37
EC1
SOFTWARE
ARG B:389 , GOL B:616 , HOH B:1207
BINDING SITE FOR RESIDUE ACT B 603
38
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
39
EC3
SOFTWARE
LYS A:354 , HIS B:150
BINDING SITE FOR RESIDUE ACT B 605
40
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
41
EC5
SOFTWARE
ARG A:384 , ARG A:389 , ASP B:427 , ARG B:457 , HOH B:954
BINDING SITE FOR RESIDUE ACT B 607
42
EC6
SOFTWARE
LYS A:335 , ARG B:341 , HOH B:1109 , HOH B:1134
BINDING SITE FOR RESIDUE ACT B 608
43
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
44
EC8
SOFTWARE
ASP B:4 , GLU B:5
BINDING SITE FOR RESIDUE GOL B 610
45
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
46
FC1
SOFTWARE
THR B:23 , PRO B:24 , GLN B:26 , HOH B:1051
BINDING SITE FOR RESIDUE ACT B 612
47
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
48
FC3
SOFTWARE
GLU A:187 , LYS B:52 , SER B:53 , TRP B:54 , HOH B:1107
BINDING SITE FOR RESIDUE GOL B 614
49
FC4
SOFTWARE
GLN B:385 , HIS B:416 , ALA B:417 , L4D B:613 , HOH B:1135
BINDING SITE FOR RESIDUE ACT B 615
50
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)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d4i9da_ (A:)
1b: SCOP_d4i9db_ (B:)
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Protein Domains
(
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(
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Organisms
(
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(
)
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
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all CATH domains
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