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1H17
Biol. Unit 1
Info
Asym.Unit (161 KB)
Biol.Unit 1 (306 KB)
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(1)
Title
:
PYRUVATE FORMATE-LYASE (E.COLI) IN COMPLEX WITH COA AND THE SUBSTRATE ANALOG OXAMATE
Authors
:
A. Becker, W. Kabsch
Date
:
03 Jul 02 (Deposition) - 01 Nov 02 (Release) - 10 Jun 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Lyase, Glycyl Radical Enzyme, Transferase, Acyltransferase Acetylation
(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
(4, 14)
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: OXAMIC ACID (OXMa)
6a: TETRAETHYLENE GLYCOL (PG4a)
6b: TETRAETHYLENE GLYCOL (PG4b)
6c: TETRAETHYLENE GLYCOL (PG4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
COA
2
Ligand/Ion
COENZYME A
2
DTL
4
Ligand/Ion
L-TREITOL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
NA
-1
Ligand/Ion
SODIUM ION
5
OXM
2
Ligand/Ion
OXAMIC ACID
6
PG4
6
Ligand/Ion
TETRAETHYLENE GLYCOL
[
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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:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:652 , LEU A:654 , GLU A:700 , GLY A:701 , HOH A:3085 , HOH A:3157
BINDING SITE FOR RESIDUE NA A9001
02
AC2
SOFTWARE
GLU A:214 , GLN A:215 , ARG A:218 , HOH A:2588 , HOH A:2912
BINDING SITE FOR RESIDUE NA A9002
03
AC3
SOFTWARE
THR A:80 , ILE A:81 , SER A:268 , HOH A:2313
BINDING SITE FOR RESIDUE NA A9003
04
AC4
SOFTWARE
LEU A:688 , HOH A:2298 , HOH A:3133 , PG4 A:9013
BINDING SITE FOR RESIDUE NA A9004
05
AC5
SOFTWARE
GLN A:589 , PRO A:599 , HOH A:2550 , HOH A:3021
BINDING SITE FOR RESIDUE NA A9005
06
AC6
SOFTWARE
MET A:58 , LYS A:62 , HOH A:2088 , HOH A:2243 , HOH A:3191
BINDING SITE FOR RESIDUE NA A9006
07
AC7
SOFTWARE
PHE A:112 , GLN A:269 , HOH A:2136 , HOH A:2138 , HOH A:2921 , HOH A:2922 , HOH A:2923 , HOH A:3252 , HOH A:3253 , HOH A:3254
BINDING SITE FOR RESIDUE NA A9007
08
AC8
SOFTWARE
COA A:1000 , HOH A:2491 , HOH A:3246
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:2491 , HOH A:2746 , HOH A:3233 , HOH A:3234 , HOH A:3235 , HOH A:3236 , HOH A:3237 , HOH A:3238 , HOH A:3240 , HOH A:3241 , HOH A:3242 , HOH A:3243 , HOH A:3244 , HOH A:3245 , HOH A:3247 , MG A:9008
BINDING SITE FOR RESIDUE COA A1000
10
BC1
SOFTWARE
ARG A:176 , ALA A:272 , ALA A:273 , CYS A:418 , PHE A:432 , ARG A:435 , LEU A:604 , ILE A:606 , HOH A:3248
BINDING SITE FOR RESIDUE OXM A1001
11
BC2
SOFTWARE
THR A:138 , GLU A:139 , LYS A:142 , GLU A:225 , ARG A:228 , GLN A:232 , HOH A:2451 , HOH A:2452 , HOH A:3249 , HOH A:3250 , HOH A:3251 , HOH A:3253
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:2282 , HOH A:3256 , HOH A:3257 , HOH A:3258 , HOH A:3259
BINDING SITE FOR RESIDUE DTL A9010
13
BC4
SOFTWARE
GLU A:40 , LEU A:43 , HOH A:3260
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:2941 , HOH A:3263 , HOH A:3265
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 only available for the asymmetric unit)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 6)
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
2
A:2-624
2
GLY_RADICAL_2
PS51149
Glycine radical domain profile.
PFLB_ECOLI
632-760
2
A:631-759
3
GLY_RADICAL_1
PS00850
Glycine radical domain signature.
PFLB_ECOLI
730-738
2
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1h17a_ (A:)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
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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
d1h17a_
A:
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1h17A00 (A:1-759)
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Classes
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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
1h17A00
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
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
Asymmetric Unit 2
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Example Commands
Example Command
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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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Asym.Unit (161 KB)
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