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4Q3B
Asym. Unit
Info
Asym.Unit (350 KB)
Biol.Unit 1 (90 KB)
Biol.Unit 2 (90 KB)
Biol.Unit 3 (89 KB)
Biol.Unit 4 (88 KB)
Biol.Unit 5 (175 KB)
Biol.Unit 6 (172 KB)
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(1)
Title
:
PYLD COCRYSTALLIZED WITH L-LYSINE-NE-D-LYSINE 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
:
1.90
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
(7, 40)
Info
All Hetero Components
1a: N~6~-[(2R)-2,3,4,5-TETRAHYDROPYRID... (2YFa)
1b: N~6~-[(2R)-2,3,4,5-TETRAHYDROPYRID... (2YFb)
1c: N~6~-[(2R)-2,3,4,5-TETRAHYDROPYRID... (2YFc)
1d: N~6~-[(2R)-2,3,4,5-TETRAHYDROPYRID... (2YFd)
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)
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)
3o: GLYCEROL (GOLo)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2YF
4
Ligand/Ion
N~6~-[(2R)-2,3,4,5-TETRAHYDROPYRIDIN-2-YLCARBONYL]-L-LYSINE
2
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
3
GOL
15
Ligand/Ion
GLYCEROL
4
MG
4
Ligand/Ion
MAGNESIUM ION
5
NA
4
Ligand/Ion
SODIUM ION
6
NAI
4
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
7
PEG
3
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
close Hetero Component info
]
Sites
(40, 40)
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: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:2 , ASN A:121 , GLY A:150 , LYS A:151 , VAL A:152 , 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 , 2YF A:904 , HOH A:1002 , HOH A:1004 , HOH A:1040 , HOH A:1101 , HOH A:1120
BINDING SITE FOR RESIDUE NAI A 901
02
AC2
SOFTWARE
GLU A:202 , THR A:204 , CYS A:206 , PRO A:227 , HOH A:1061
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 , ASP A:104 , ASN A:121 , PRO A:246 , NAI A:901 , HOH A:1010 , HOH A:1024 , HOH A:1031 , HOH A:1051 , HOH A:1101
BINDING SITE FOR RESIDUE 2YF A 904
05
AC5
SOFTWARE
SER A:134 , TYR A:136 , ALA A:139 , SER A:141
BINDING SITE FOR RESIDUE EDO A 905
06
AC6
SOFTWARE
SER A:45 , GLN A:72 , GLY A:75 , PHE A:76 , ASP A:164 , HOH A:1052
BINDING SITE FOR RESIDUE GOL A 906
07
AC7
SOFTWARE
THR A:5 , ASP A:7
BINDING SITE FOR RESIDUE GOL A 907
08
AC8
SOFTWARE
LYS A:18 , ALA A:19 , ALA A:22 , LEU A:242 , ALA A:244 , HOH A:1111 , HOH A:1116
BINDING SITE FOR RESIDUE GOL A 908
09
AC9
SOFTWARE
LEU A:38 , TYR A:39 , HOH A:1062 , HOH A:1112 , HOH A:1118 , ARG B:135
BINDING SITE FOR RESIDUE GOL A 909
10
BC1
SOFTWARE
PHE A:165 , ARG A:166 , VAL A:167 , GLY A:185 , ILE A:187
BINDING SITE FOR RESIDUE GOL A 910
11
BC2
SOFTWARE
PHE A:154 , HOH A:1044
BINDING SITE FOR RESIDUE GOL A 911
12
BC3
SOFTWARE
GLU A:131 , SER A:134 , LYS A:163 , PHE A:165 , HOH A:1089 , HOH A:1128
BINDING SITE FOR RESIDUE GOL A 912
13
BC4
SOFTWARE
SER A:21 , HOH A:1077 , LYS B:47 , PHE B:79 , EDO B:906
BINDING SITE FOR RESIDUE GOL A 913
14
BC5
SOFTWARE
ALA B:2 , ASN B:121 , THR B:125 , GLY B:150 , LYS B:151 , VAL B:152 , TYR B:170 , ASP B:171 , ALA B:172 , ASP B:173 , ALA B:203 , THR B:204 , PRO B:205 , THR B:209 , PRO B:224 , ILE B:226 , GLU B:245 , PRO B:246 , LEU B:247 , MG B:903 , 2YF B:904 , HOH B:1002 , HOH B:1050 , HOH B:1060 , HOH B:1113 , HOH B:1119 , HOH B:1129 , HOH B:1130
BINDING SITE FOR RESIDUE NAI B 901
15
BC6
SOFTWARE
GLU B:202 , THR B:204 , CYS B:206 , PRO B:227 , HOH B:1009
BINDING SITE FOR RESIDUE NA B 902
16
BC7
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
17
BC8
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 , ASN B:121 , PRO B:246 , NAI B:901 , HOH B:1006 , HOH B:1010 , HOH B:1034 , HOH B:1052 , HOH B:1113
BINDING SITE FOR RESIDUE 2YF B 904
18
BC9
SOFTWARE
LYS B:32 , LYS B:36 , SER B:43 , HOH B:1061
BINDING SITE FOR RESIDUE EDO B 905
19
CC1
SOFTWARE
GLN A:17 , GOL A:913 , HOH A:1078 , ASP B:82 , GLU B:91 , ASN B:95
BINDING SITE FOR RESIDUE EDO B 906
20
CC2
SOFTWARE
ALA A:192 , LYS B:196 , GLU B:217
BINDING SITE FOR RESIDUE EDO B 907
21
CC3
SOFTWARE
THR B:41 , PHE B:42 , LEU B:259 , HOH B:1029 , HOH B:1036
BINDING SITE FOR RESIDUE GOL B 908
22
CC4
SOFTWARE
GLU A:158 , VAL A:161 , GLN A:162 , ASN A:183 , LEU A:184 , LYS B:36 , THR B:41 , PHE B:42
BINDING SITE FOR RESIDUE GOL B 909
23
CC5
SOFTWARE
LEU B:9 , ILE B:10 , ASN B:11 , ILE B:12 , ASN B:62 , ALA B:65 , SER B:66 , PEG B:916 , HOH B:1057
BINDING SITE FOR RESIDUE GOL B 910
24
CC6
SOFTWARE
LYS A:32 , TYR A:73 , HOH A:1012 , GLN B:72 , ASP B:77 , SER B:78 , HOH B:1117 , HOH B:1125
BINDING SITE FOR RESIDUE GOL B 911
25
CC7
SOFTWARE
LEU B:38
BINDING SITE FOR RESIDUE GOL B 912
26
CC8
SOFTWARE
ALA B:19 , ARG B:235 , LEU B:242 , ALA B:244
BINDING SITE FOR RESIDUE GOL B 913
27
CC9
SOFTWARE
ALA A:37 , ARG A:135 , LYS A:163 , GLN B:24 , GLU B:25 , GLY B:28 , HOH B:1088
BINDING SITE FOR RESIDUE PEG B 914
28
DC1
SOFTWARE
VAL A:53 , ASP A:85 , MET A:102 , ASP B:85 , MET B:102
BINDING SITE FOR RESIDUE PEG B 915
29
DC2
SOFTWARE
LEU A:9 , ASN A:11 , ILE A:12 , ASN A:62 , ALA A:65 , SER A:66 , ALA A:69 , HOH A:1086 , ASN B:13 , GOL B:910 , HOH B:1019 , HOH B:1056 , HOH B:1059
BINDING SITE FOR RESIDUE PEG B 916
30
DC3
SOFTWARE
ALA B:207 , ALA C:2 , ASN C:121 , THR C:125 , GLY C:150 , LYS C:151 , VAL C:152 , ASP C:171 , ALA C:172 , ASP C:173 , LEU C:176 , 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 , 2YF C:904 , EDO C:905 , HOH C:1008 , HOH C:1018
BINDING SITE FOR RESIDUE NAI C 901
31
DC4
SOFTWARE
GLU C:202 , THR C:204 , CYS C:206 , PRO C:227 , ALA C:229 , HOH C:1017
BINDING SITE FOR RESIDUE NA C 902
32
DC5
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
33
DC6
SOFTWARE
LEU C:3 , LEU C:4 , PRO C:52 , VAL C:53 , GLY C:58 , ILE C:59 , ILE C:60 , PHE C:63 , ALA C:103 , LEU C:247 , NAI C:901 , EDO C:905 , HOH C:1007 , HOH C:1009 , HOH C:1012
BINDING SITE FOR RESIDUE 2YF C 904
34
DC7
SOFTWARE
ASP C:105 , GLN C:122 , NAI C:901 , 2YF C:904
BINDING SITE FOR RESIDUE EDO C 905
35
DC8
SOFTWARE
LYS D:36
BINDING SITE FOR RESIDUE EDO C 906
36
DC9
SOFTWARE
ALA D:2 , ASN D:121 , THR D:125 , VAL D:147 , GLY D:150 , LYS D:151 , VAL D:152 , TYR D:170 , ASP D:171 , ALA D:172 , LEU D:176 , ALA D:203 , THR D:204 , PRO D:205 , CYS D:206 , THR D:209 , PRO D:224 , ILE D:226 , GLU D:245 , PRO D:246 , LEU D:247 , MG D:903 , 2YF D:904 , HOH D:1004 , HOH D:1016 , HOH D:1017 , HOH D:1025
BINDING SITE FOR RESIDUE NAI D 901
37
EC1
SOFTWARE
GLU D:202 , THR D:204 , CYS D:206 , PRO D:227 , ALA D:229 , HOH D:1008
BINDING SITE FOR RESIDUE NA D 902
38
EC2
SOFTWARE
TYR D:129 , GLU D:245 , LEU D:247 , ILE D:249 , GLY D:250 , NAI D:901
BINDING SITE FOR RESIDUE MG D 903
39
EC3
SOFTWARE
LEU D:3 , LEU D:4 , PRO D:52 , VAL D:53 , GLY D:58 , ILE D:59 , ILE D:60 , PHE D:63 , ALA D:103 , ASN D:121 , NAI D:901 , HOH D:1001 , HOH D:1005 , HOH D:1020 , HOH D:1022
BINDING SITE FOR RESIDUE 2YF D 904
40
EC4
SOFTWARE
ASP D:85 , TYR D:89 , MET D:102
BINDING SITE FOR RESIDUE GOL D 905
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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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.
SCOP Domains
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CATH Domains
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all 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 (350 KB)
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