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3MVY
Asym. Unit
Info
Asym.Unit (175 KB)
Biol.Unit 1 (88 KB)
Biol.Unit 2 (86 KB)
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(1)
Title
:
X-RAY STRUCTURE OF THE DIATOMIC OXO-INTERMEDIATE NIKA/1-INT', PRIOR HYDROXYLATION
Authors
:
C. Cavazza, C. Bochot, P. Rousselot-Pailley, P. Carpentier, M. V. Cher L. Martin, C. Marchi-Delapierre, J. C. Fontecilla-Camps, S. Menage
Date
:
05 May 10 (Deposition) - 09 Feb 11 (Release) - 09 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Protein-Bound Iron Complex, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Cavazza, C. Bochot, P. Rousselot-Pailley, P. Carpentier, M. V. Cherrier, L. Martin, C. Marchi-Delapierre, J. C. Fontecilla-Camps, S. Menage
Crystallographic Snapshots Of The Reaction Of Aromatic C-H With O(2) Catalysed By A Protein-Bound Iron Complex
Nat. Chem. V. 2 1069 2010
[
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Hetero Components
(7, 24)
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)
2a: 2-[2-[CARBOXYMETHYL(PHENYLMETHYL)A... (BHZa)
2b: 2-[2-[CARBOXYMETHYL(PHENYLMETHYL)A... (BHZb)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
4a: FE (III) ION (FEa)
4b: FE (III) ION (FEb)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
5d: GLYCEROL (GOLd)
5e: GLYCEROL (GOLe)
5f: GLYCEROL (GOLf)
5g: GLYCEROL (GOLg)
5h: GLYCEROL (GOLh)
6a: PEROXIDE ION (PERa)
6b: PEROXIDE ION (PERb)
7a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
7
Ligand/Ion
ACETATE ION
2
BHZ
2
Ligand/Ion
2-[2-[CARBOXYMETHYL(PHENYLMETHYL)AMINO]ETHYL-[(2-HYDROXYPHENYL)METHYL]AMINO]ETHANOIC ACID
3
CL
2
Ligand/Ion
CHLORIDE ION
4
FE
2
Ligand/Ion
FE (III) ION
5
GOL
8
Ligand/Ion
GLYCEROL
6
PER
2
Ligand/Ion
PEROXIDE ION
7
SO4
1
Ligand/Ion
SULFATE ION
[
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Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:52 , ASP A:69
BINDING SITE FOR RESIDUE ACT A 503
02
AC2
SOFTWARE
ASN A:261 , GLU A:262 , LEU A:263 , HOH A:689
BINDING SITE FOR RESIDUE ACT A 504
03
AC3
SOFTWARE
ASN A:235 , ALA A:237 , GLN A:423 , HOH A:680
BINDING SITE FOR RESIDUE ACT A 505
04
AC4
SOFTWARE
ARG A:384 , ARG A:389 , LEU B:430 , ARG B:457
BINDING SITE FOR RESIDUE SO4 A 506
05
AC5
SOFTWARE
PRO A:159 , LEU A:167 , GLN A:168 , HOH A:721 , ALA B:208 , THR B:211
BINDING SITE FOR RESIDUE GOL A 507
06
AC6
SOFTWARE
ASN A:149 , LYS A:157 , HOH A:640
BINDING SITE FOR RESIDUE GOL A 508
07
AC7
SOFTWARE
GLU A:358 , GLN A:361 , LEU A:373 , HOH B:606
BINDING SITE FOR RESIDUE GOL A 509
08
AC8
SOFTWARE
BHZ A:511 , PER A:512
BINDING SITE FOR RESIDUE FE A 510
09
AC9
SOFTWARE
TYR A:22 , MET A:27 , ARG A:97 , TRP A:100 , ARG A:137 , TRP A:398 , HIS A:416 , THR A:490 , FE A:510 , PER A:512 , HOH A:544 , HOH A:612 , HOH A:620
BINDING SITE FOR RESIDUE BHZ A 511
10
BC1
SOFTWARE
ARG A:137 , FE A:510 , BHZ A:511
BINDING SITE FOR RESIDUE PER A 512
11
BC2
SOFTWARE
HIS A:442 , ASP A:443
BINDING SITE FOR RESIDUE CL A 513
12
BC3
SOFTWARE
ASN A:220 , ILE A:246 , GLU A:247 , ARG A:396 , ALA A:489 , THR A:490 , GOL A:516
BINDING SITE FOR RESIDUE GOL A 515
13
BC4
SOFTWARE
PRO A:11 , GLY A:219 , ASN A:220 , GLY A:222 , LEU A:223 , GOL A:515
BINDING SITE FOR RESIDUE GOL A 516
14
BC5
SOFTWARE
ARG A:89 , ASP A:109 , VAL A:110 , ASN A:281 , HOH A:723
BINDING SITE FOR RESIDUE ACT A 517
15
BC6
SOFTWARE
PHE A:28 , SER A:31 , ARG A:140 , GLU A:491 , ILE A:492 , GLU A:495
BINDING SITE FOR RESIDUE GOL A 518
16
BC7
SOFTWARE
THR B:23 , GLN B:26 , GLU B:378
BINDING SITE FOR RESIDUE ACT B 503
17
BC8
SOFTWARE
ASN B:274 , LYS B:275 , LYS B:276 , TYR B:310
BINDING SITE FOR RESIDUE ACT B 504
18
BC9
SOFTWARE
PRO B:11 , GLY B:219 , ASN B:220 , GLY B:222
BINDING SITE FOR RESIDUE GOL B 505
19
CC1
SOFTWARE
BHZ B:507 , PER B:508
BINDING SITE FOR RESIDUE FE B 506
20
CC2
SOFTWARE
TYR B:22 , MET B:27 , ARG B:97 , TRP B:100 , ARG B:137 , TRP B:398 , THR B:490 , FE B:506 , PER B:508 , HOH B:547 , HOH B:609 , HOH B:669
BINDING SITE FOR RESIDUE BHZ B 507
21
CC3
SOFTWARE
ARG B:137 , FE B:506 , BHZ B:507
BINDING SITE FOR RESIDUE PER B 508
22
CC4
SOFTWARE
ARG A:97 , HOH A:596 , LYS B:314
BINDING SITE FOR RESIDUE ACT B 509
23
CC5
SOFTWARE
GLU B:221 , VAL B:249 , SER B:353 , MET B:356 , PHE B:394 , HIS B:395
BINDING SITE FOR RESIDUE GOL B 510
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: SBP_BACTERIAL_5 (A:51-73,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
2
A:51-73
B:51-73
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
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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_d3mvya_ (A:)
1b: SCOP_d3mvyb_ (B:)
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Classes
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Families
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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
d3mvya_
A:
1b
d3mvyb_
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
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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Show PDB file:
Asym.Unit (175 KB)
Header - Asym.Unit
Biol.Unit 1 (88 KB)
Header - Biol.Unit 1
Biol.Unit 2 (86 KB)
Header - Biol.Unit 2
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