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4Q3A
Biol. Unit 5
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
[
close entry info
]
Hetero Components
(6, 19)
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:
Select:
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
7
Ligand/Ion
1,2-ETHANEDIOL
3
GOL
6
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
2
Ligand/Ion
DI(HYDROXYETHYL)ETHER
8
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(38, 38)
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: EC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:2 , ASN A:121 , THR A:125 , GLY A:150 , LYS A:151 , VAL A:152 , TYR A:170 , ASP A:171 , ALA A:172 , ALA A:203 , THR A:204 , PRO A:205 , CYS A:206 , THR A:209 , PRO A:224 , ILE A:226 , GLU A:245 , PRO A:246 , LEU A:247 , MG A:903 , HOH A:1001 , HOH A:1002 , HOH A:1040 , HOH A:1042 , HOH A:1045 , HOH A:1101 , ALA D:207
BINDING SITE FOR RESIDUE NAI A 901
02
AC2
SOFTWARE
GLU A:202 , THR A:204 , CYS A:206 , PRO A:227
BINDING SITE FOR RESIDUE NA A 902
03
AC3
SOFTWARE
TYR A:129 , GLU A:245 , LEU A:247 , ILE A:249 , GLY A:250 , NAI A:901
BINDING SITE FOR RESIDUE MG A 903
04
AC4
SOFTWARE
LEU A:3 , LEU A:4 , VAL A:53 , GLY A:58 , ILE A:59 , ILE A:60 , PHE A:63 , ALA A:103 , ASN A:121 , PRO A:246 , HOH A:1004 , HOH A:1006 , HOH A:1017 , HOH A:1044 , HOH A:1065 , HOH A:1080
BINDING SITE FOR RESIDUE 2YC A 904
05
AC5
SOFTWARE
GLU A:158 , GLN A:162 , LYS B:36 , GLY B:40 , THR B:41 , PHE B:42 , HOH B:1029
BINDING SITE FOR RESIDUE GOL A 905
06
AC6
SOFTWARE
ASP A:85 , ASP B:85 , MET B:102
BINDING SITE FOR RESIDUE GOL A 906
07
AC7
SOFTWARE
ALA A:37 , GLU A:131 , ARG A:135 , HIS A:159 , EDO A:915
BINDING SITE FOR RESIDUE GOL A 907
08
AC8
SOFTWARE
ALA A:19 , ARG A:235 , LEU A:242 , ALA A:244
BINDING SITE FOR RESIDUE GOL A 908
09
AC9
SOFTWARE
LEU A:9 , ILE A:10 , ASN A:11 , ILE A:12 , ALA A:65 , HOH A:1126
BINDING SITE FOR RESIDUE GOL A 909
10
BC1
SOFTWARE
SER A:45 , GLN A:72 , GLY A:75 , LYS B:32 , GLN B:72 , TYR B:73 , GLY B:75 , SO4 B:911
BINDING SITE FOR RESIDUE GOL A 910
11
BC2
SOFTWARE
GLN A:72 , ASP A:77 , ASP B:20 , LYS B:32 , TYR B:73 , HOH B:1031
BINDING SITE FOR RESIDUE GOL A 911
12
BC3
SOFTWARE
LYS A:117 , MET A:118 , ALA A:119 , SER A:257
BINDING SITE FOR RESIDUE PEG A 912
13
BC4
SOFTWARE
PHE A:165 , VAL A:167 , GLY A:185
BINDING SITE FOR RESIDUE EDO A 913
14
BC5
SOFTWARE
SER A:134 , ARG A:135 , LYS A:163 , PHE A:165
BINDING SITE FOR RESIDUE EDO A 914
15
BC6
SOFTWARE
LEU A:38 , ILE A:127 , GOL A:907 , HOH A:1114
BINDING SITE FOR RESIDUE EDO A 915
16
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
17
BC8
SOFTWARE
GLU B:202 , THR B:204 , CYS B:206 , GLY B:225 , PRO B:227 , HOH B:1058
BINDING SITE FOR RESIDUE NA B 902
18
BC9
SOFTWARE
TYR B:129 , GLU B:245 , LEU B:247 , ILE B:249 , GLY B:250 , NAI B:901
BINDING SITE FOR RESIDUE MG B 903
19
CC1
SOFTWARE
LEU B:3 , LEU B:4 , VAL B:53 , GLY B:58 , ILE B:59 , ILE B:60 , PHE B:63 , ALA B:103 , ASP B:104 , ASN B:121 , PRO B:246 , NAI B:901 , HOH B:1002 , HOH B:1006 , HOH B:1036 , HOH B:1039 , HOH B:1041 , HOH B:1042
BINDING SITE FOR RESIDUE 2YC B 904
20
CC2
SOFTWARE
LYS A:142 , LYS A:163 , GLN B:24 , GLY B:28 , LEU B:29
BINDING SITE FOR RESIDUE GOL B 905
21
CC3
SOFTWARE
THR B:41 , PHE B:42 , LEU B:259 , HOH B:1019 , HOH B:1034
BINDING SITE FOR RESIDUE GOL B 906
22
CC4
SOFTWARE
GLY B:61 , ASN B:62 , PHE B:63 , SER B:64 , ALA B:65 , HOH B:1055
BINDING SITE FOR RESIDUE GOL B 907
23
CC5
SOFTWARE
LYS A:32 , TYR A:73 , HOH A:1035 , HOH A:1124 , HOH A:1125 , GLN B:72 , ASP B:77 , SO4 B:911
BINDING SITE FOR RESIDUE GOL B 908
24
CC6
SOFTWARE
LEU B:9 , ILE B:10 , ASN B:11 , ILE B:12 , ALA B:65
BINDING SITE FOR RESIDUE GOL B 909
25
CC7
SOFTWARE
LYS B:18 , ALA B:19 , LEU B:242 , ALA B:244 , HOH B:1050
BINDING SITE FOR RESIDUE GOL B 910
26
CC8
SOFTWARE
LYS A:32 , TYR A:73 , GLY A:75 , GOL A:910 , SER B:45 , GLN B:72 , PHE B:76 , GOL B:908
BINDING SITE FOR RESIDUE SO4 B 911
27
CC9
SOFTWARE
ALA B:37 , LEU B:38 , GLU B:131 , ARG B:135 , LYS B:163 , HOH B:1094
BINDING SITE FOR RESIDUE SO4 B 912
28
DC1
SOFTWARE
MET B:118 , CYS B:124 , SER B:257 , HOH B:1053
BINDING SITE FOR RESIDUE PEG B 913
29
DC2
SOFTWARE
LEU A:113 , LYS A:114 , LEU B:113 , LYS B:114
BINDING SITE FOR RESIDUE PEG B 914
30
DC3
SOFTWARE
PHE B:165 , VAL B:167 , GLY B:185
BINDING SITE FOR RESIDUE EDO B 915
31
DC4
SOFTWARE
GLN A:17 , SER A:21 , HOH A:1060 , HOH A:1087 , HOH A:1099 , LYS B:47
BINDING SITE FOR RESIDUE EDO B 916
32
DC5
SOFTWARE
PRO B:52 , ASP B:82
BINDING SITE FOR RESIDUE EDO B 917
33
DC6
SOFTWARE
VAL A:80 , GLU A:91 , ASN A:95 , GLN B:17
BINDING SITE FOR RESIDUE EDO B 918
34
DC7
SOFTWARE
LEU B:149 , GLY B:150 , LEU B:176 , ARG B:179
BINDING SITE FOR RESIDUE EDO B 919
35
DC8
SOFTWARE
SER B:44 , GLU B:98 , LYS B:114
BINDING SITE FOR RESIDUE EDO B 920
36
DC9
SOFTWARE
LEU B:38
BINDING SITE FOR RESIDUE EDO B 921
37
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
38
EC9
SOFTWARE
HOH A:1059 , ALA D:2 , ASN D:121 , GLN D:122 , THR D:125 , VAL D:147 , GLY D:150 , LYS D:151 , VAL D:152 , TYR D:170 , ASP D:171 , ALA D:172 , ALA D:203 , THR D:204 , PRO D:205 , THR D:209 , PRO D:224 , ILE D:226 , GLU D:245 , PRO D:246 , LEU D:247 , MG D:903 , HOH D:1002 , HOH D:1004 , HOH D:1011
BINDING SITE FOR RESIDUE NAI D 901
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
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;
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[
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Exons
(0, 0)
Info
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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
(0, 0)
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CATH Domains
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Pfam Domains
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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 (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
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