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1H16
Asym. Unit
Info
Asym.Unit (161 KB)
Biol.Unit 1 (305 KB)
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(1)
Title
:
PYRUVATE FORMATE-LYASE (E.COLI) IN COMPLEX WITH PYRUVATE AND COA
Authors
:
A. Becker, W. Kabsch
Date
:
03 Jul 02 (Deposition) - 01 Nov 02 (Release) - 10 Jun 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.53
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Lyase, Glycyl Radical Enzyme, Transferase, Acyltransferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Becker, W. Kabsch
X-Ray Structure Of Pyruvate Formate-Lyase In Complex With Pyruvate And Coa. How The Enzyme Uses The Cys-418 Thiyl Radical For Pyruvate Cleavage
J. Biol. Chem. V. 277 40036 2002
[
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Hetero Components
(6, 15)
Info
All Hetero Components
1a: COENZYME A (COAa)
2a: L-TREITOL (DTLa)
2b: L-TREITOL (DTLb)
3a: MAGNESIUM ION (MGa)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
4e: SODIUM ION (NAe)
4f: SODIUM ION (NAf)
4g: SODIUM ION (NAg)
5a: TETRAETHYLENE GLYCOL (PG4a)
5b: TETRAETHYLENE GLYCOL (PG4b)
5c: TETRAETHYLENE GLYCOL (PG4c)
6a: PYRUVIC ACID (PYRa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
COA
1
Ligand/Ion
COENZYME A
2
DTL
2
Ligand/Ion
L-TREITOL
3
MG
1
Ligand/Ion
MAGNESIUM ION
4
NA
7
Ligand/Ion
SODIUM ION
5
PG4
3
Ligand/Ion
TETRAETHYLENE GLYCOL
6
PYR
1
Ligand/Ion
PYRUVIC ACID
[
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]
Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:652 , LEU A:654 , GLU A:700 , GLY A:701 , HOH A:3157 , HOH A:3160
BINDING SITE FOR RESIDUE NA A9001
02
AC2
SOFTWARE
GLU A:214 , GLN A:215 , ARG A:218 , HOH A:2595 , HOH A:2920
BINDING SITE FOR RESIDUE NA A9002
03
AC3
SOFTWARE
THR A:80 , ILE A:81 , SER A:268 , HOH A:2138 , HOH A:2140 , HOH A:2327 , HOH A:2330
BINDING SITE FOR RESIDUE NA A9003
04
AC4
SOFTWARE
HOH A:2624 , HOH A:3136 , PG4 A:9013
BINDING SITE FOR RESIDUE NA A9004
05
AC5
SOFTWARE
GLN A:589 , PRO A:599 , HOH A:2558 , HOH A:3027
BINDING SITE FOR RESIDUE NA A9005
06
AC6
SOFTWARE
LYS A:62 , HOH A:2101 , HOH A:2258 , HOH A:3192
BINDING SITE FOR RESIDUE NA A9006
07
AC7
SOFTWARE
PHE A:112 , HOH A:2138 , HOH A:2689 , HOH A:2933 , HOH A:3256 , HOH A:3257
BINDING SITE FOR RESIDUE NA A9007
08
AC8
SOFTWARE
COA A:1000 , HOH A:2498 , HOH A:3250
BINDING SITE FOR RESIDUE MG A9008
09
AC9
SOFTWARE
LYS A:116 , MET A:117 , ASN A:145 , GLN A:146 , PHE A:149 , ASP A:150 , TYR A:152 , ARG A:160 , LYS A:161 , PHE A:200 , HIS A:227 , HOH A:2498 , HOH A:2744 , HOH A:3237 , HOH A:3238 , HOH A:3239 , HOH A:3240 , HOH A:3241 , HOH A:3242 , HOH A:3244 , HOH A:3245 , HOH A:3246 , HOH A:3247 , HOH A:3248 , HOH A:3249 , HOH A:3251 , MG A:9008
BINDING SITE FOR RESIDUE COA A1000
10
BC1
SOFTWARE
ARG A:176 , ALA A:273 , CYS A:418 , PHE A:432 , ARG A:435 , LEU A:604 , ILE A:606 , HOH A:3252
BINDING SITE FOR RESIDUE PYR A1001
11
BC2
SOFTWARE
THR A:138 , GLU A:139 , LYS A:142 , GLU A:225 , ARG A:228 , GLN A:232 , HOH A:2454 , HOH A:2455 , HOH A:3253 , HOH A:3254 , HOH A:3255 , HOH A:3256 , HOH A:3257
BINDING SITE FOR RESIDUE DTL A9009
12
BC3
SOFTWARE
HIS A:68 , PRO A:70 , TYR A:125 , ASP A:324 , ASP A:330 , SER A:741 , HOH A:2297 , HOH A:3259 , HOH A:3260 , HOH A:3261 , HOH A:3262
BINDING SITE FOR RESIDUE DTL A9010
13
BC4
SOFTWARE
GLU A:40
BINDING SITE FOR RESIDUE PG4 A9011
14
BC5
SOFTWARE
ALA A:198 , GLN A:199 , SER A:202 , ARG A:516 , ASP A:517 , HOH A:3266
BINDING SITE FOR RESIDUE PG4 A9012
15
BC6
SOFTWARE
LEU A:648 , THR A:649 , LEU A:688 , GLY A:691 , TYR A:692 , HOH A:3267 , NA A:9004
BINDING SITE FOR RESIDUE PG4 A9013
[
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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
(3, 3)
Info
All PROSITE Patterns/Profiles
1: PFL (A:2-624)
2: GLY_RADICAL_2 (A:631-759)
3: GLY_RADICAL_1 (A:729-737)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PFL
PS51554
Pyruvate formate-lyase domain profile.
PFLB_ECOLI
3-625
1
A:2-624
2
GLY_RADICAL_2
PS51149
Glycine radical domain profile.
PFLB_ECOLI
632-760
1
A:631-759
3
GLY_RADICAL_1
PS00850
Glycine radical domain signature.
PFLB_ECOLI
730-738
1
A:729-737
[
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]
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.
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1h16a_ (A:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PFL-like glycyl radical enzymes
(32)
Superfamily
:
PFL-like glycyl radical enzymes
(32)
Family
:
PFL-like
(11)
Protein domain
:
Pyruvate formate-lyase, PFL
(8)
Escherichia coli [TaxId: 562]
(8)
1a
d1h16a_
A:
[
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1h16A00 (A:1-759)
View:
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Classes
(
)
(
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Architectures
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)
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)
Topologies
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)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
(15)
Homologous Superfamily
:
[code=3.20.70.20, no name defined]
(15)
Escherichia coli. Organism_taxid: 562
(6)
1a
1h16A00
A:1-759
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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Atom Selection
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Protein
Nucleic
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Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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select :A, :C
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
select 5-10:A
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)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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