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4Q3A
Biol. Unit 3
Info
Asym.Unit (357 KB)
Biol.Unit 1 (91 KB)
Biol.Unit 2 (92 KB)
Biol.Unit 3 (91 KB)
Biol.Unit 4 (91 KB)
Biol.Unit 5 (177 KB)
Biol.Unit 6 (176 KB)
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(1)
Title
:
PYLD COCRYSTALLIZED WITH L-LYSINE-NE-3S-METHYL-L-ORNITHINE AND NAD+
Authors
:
F. Quitterer, P. Beck, A. Bacher, M. Groll
Date
:
11 Apr 14 (Deposition) - 23 Apr 14 (Release) - 20 Aug 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: A,B (1x)
Biol. Unit 6: C,D (1x)
Keywords
:
Rossmann Fold, Dehydrogenase, Pyrrolysine, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Quitterer, P. Beck, A. Bacher, M. Groll
The Formation Of Pyrroline And Tetrahydropyridine Rings In Amino Acids Catalyzed By Pyrrolysine Synthase (Pyld).
Angew. Chem. Int. Ed. Engl. V. 53 8150 2014
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Hetero Components
(4, 6)
Info
All Hetero Components
1a: N~6~-{[(2S,3S)-3-METHYL-3,4-DIHYDR... (2YCa)
1b: N~6~-{[(2S,3S)-3-METHYL-3,4-DIHYDR... (2YCb)
1c: N~6~-{[(2S,3S)-3-METHYL-3,4-DIHYDR... (2YCc)
1d: N~6~-{[(2S,3S)-3-METHYL-3,4-DIHYDR... (2YCd)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
6a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
6b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
6c: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIc)
6d: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAId)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
5d: SODIUM ION (NAd)
7a: DI(HYDROXYETHYL)ETHER (PEGa)
7b: DI(HYDROXYETHYL)ETHER (PEGb)
7c: DI(HYDROXYETHYL)ETHER (PEGc)
8a: SULFATE ION (SO4a)
8b: SULFATE ION (SO4b)
View:
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Label:
No.
Name
Count
Type
Full Name
1
2YC
1
Ligand/Ion
N~6~-{[(2S,3S)-3-METHYL-3,4-DIHYDRO-2H-PYRROL-2-YL]CARBONYL}-L-LYSINE
2
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
3
GOL
1
Ligand/Ion
GLYCEROL
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
NA
-1
Ligand/Ion
SODIUM ION
6
NAI
1
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
7
PEG
-1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
8
SO4
-1
Ligand/Ion
SULFATE ION
[
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Sites
(9, 9)
Info
All Sites
1: BC7 (SOFTWARE)
2: EC1 (SOFTWARE)
3: EC2 (SOFTWARE)
4: EC3 (SOFTWARE)
5: EC4 (SOFTWARE)
6: EC5 (SOFTWARE)
7: EC6 (SOFTWARE)
8: EC7 (SOFTWARE)
9: EC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
BC7
SOFTWARE
ALA B:2 , ASN B:121 , GLN B:122 , THR B:125 , GLY B:150 , LYS B:151 , VAL B:152 , ASP B:171 , ALA B:172 , ASP B:173 , ALA B:203 , THR B:204 , PRO B:205 , CYS B:206 , THR B:209 , PRO B:224 , ILE B:226 , GLU B:245 , PRO B:246 , LEU B:247 , MG B:903 , 2YC B:904 , HOH B:1001 , HOH B:1005 , HOH B:1032 , HOH B:1062 , HOH B:1108 , ALA C:207 , HOH C:1015
BINDING SITE FOR RESIDUE NAI B 901
2
EC1
SOFTWARE
ALA B:207 , ALA C:2 , ASN C:121 , GLN C:122 , THR C:125 , GLY C:150 , LYS C:151 , VAL C:152 , TYR C:170 , ASP C:171 , ALA C:172 , ASP C:173 , ALA C:203 , THR C:204 , PRO C:205 , PRO C:224 , ILE C:226 , GLU C:245 , PRO C:246 , LEU C:247 , MG C:903 , 2YC C:904 , HOH C:1002 , HOH C:1003 , HOH C:1009 , HOH C:1018 , HOH C:1030
BINDING SITE FOR RESIDUE NAI C 901
3
EC2
SOFTWARE
GLU C:202 , THR C:204 , CYS C:206 , PRO C:227 , HOH C:1039
BINDING SITE FOR RESIDUE NA C 902
4
EC3
SOFTWARE
TYR C:129 , GLU C:245 , LEU C:247 , ILE C:249 , GLY C:250 , NAI C:901
BINDING SITE FOR RESIDUE MG C 903
5
EC4
SOFTWARE
LEU C:3 , LEU C:4 , PRO C:52 , VAL C:53 , GLY C:58 , ILE C:59 , ILE C:60 , ALA C:103 , ASN C:121 , NAI C:901 , HOH C:1001 , HOH C:1005 , HOH C:1007 , HOH C:1044
BINDING SITE FOR RESIDUE 2YC C 904
6
EC5
SOFTWARE
ASP C:85 , ASP D:85 , MET D:102
BINDING SITE FOR RESIDUE GOL C 905
7
EC6
SOFTWARE
MET C:1 , ALA C:2 , PRO C:205
BINDING SITE FOR RESIDUE EDO C 906
8
EC7
SOFTWARE
ILE C:59 , ILE C:60 , GLY C:61
BINDING SITE FOR RESIDUE EDO C 907
9
EC8
SOFTWARE
LEU C:242 , ILE C:243 , ALA C:244
BINDING SITE FOR RESIDUE EDO C 908
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(0, 0)
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CATH Domains
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Pfam Domains
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Chain C
Asymmetric Unit 1
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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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In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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Show PDB file:
Asym.Unit (357 KB)
Header - Asym.Unit
Biol.Unit 1 (91 KB)
Header - Biol.Unit 1
Biol.Unit 2 (92 KB)
Header - Biol.Unit 2
Biol.Unit 3 (91 KB)
Header - Biol.Unit 3
Biol.Unit 4 (91 KB)
Header - Biol.Unit 4
Biol.Unit 5 (177 KB)
Header - Biol.Unit 5
Biol.Unit 6 (176 KB)
Header - Biol.Unit 6
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