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3O0D
Asym. Unit
Info
Asym.Unit (386 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (62 KB)
Biol.Unit 3 (61 KB)
Biol.Unit 4 (59 KB)
Biol.Unit 5 (62 KB)
Biol.Unit 6 (60 KB)
Biol.Unit 7 (54 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF LIP2 LIPASE FROM YARROWIA LIPOLYTICA AT 1.7 A RESOLUTION
Authors
:
F. Bordes, S. Tranier, L. Mourey, A. Marty
Date
:
19 Jul 10 (Deposition) - 24 Nov 10 (Release) - 24 Nov 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E,F,G
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: G (1x)
Keywords
:
Alpha/Beta-Hydrolase, Lipase, Lipids Binding, Glycosylation, Extracellular, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Bordes, S. Barbe, P. Escalier, L. Mourey, I. Andre, A. Marty, S. Tranier
Exploring The Conformational States And Rearrangements Of Yarrowia Lipolytica Lipase.
Biophys. J. V. 99 2225 2010
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Hetero Components
(4, 38)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
1e: POTASSIUM ION (Ke)
1f: POTASSIUM ION (Kf)
1g: POTASSIUM ION (Kg)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
2c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
2d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
2e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
2f: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDf)
2g: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDg)
2h: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDh)
2i: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDi)
2j: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDj)
2k: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDk)
2l: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDl)
2m: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDm)
3a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
3b: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDb)
3c: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDc)
3d: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDd)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4i: N-ACETYL-D-GLUCOSAMINE (NAGi)
4j: N-ACETYL-D-GLUCOSAMINE (NAGj)
4k: N-ACETYL-D-GLUCOSAMINE (NAGk)
4l: N-ACETYL-D-GLUCOSAMINE (NAGl)
4m: N-ACETYL-D-GLUCOSAMINE (NAGm)
4n: N-ACETYL-D-GLUCOSAMINE (NAGn)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
7
Ligand/Ion
POTASSIUM ION
2
MPD
13
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
MRD
4
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
4
NAG
14
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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: EC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:113 , TYR A:137 , GLY A:141 , ASP A:145 , ASN A:174 , LEU A:175 , ASN A:178 , HIS A:180
BINDING SITE FOR RESIDUE NAG A 302
02
AC2
SOFTWARE
LEU A:110 , ALA A:112 , ILE A:130 , ASN A:134 , ASN A:138 , HOH A:829 , HOH A:1201 , HOH A:1579
BINDING SITE FOR RESIDUE NAG A 303
03
AC3
SOFTWARE
GLN A:282 , HOH A:343 , HOH A:359 , THR C:117 , ALA C:118 , HOH C:644
BINDING SITE FOR RESIDUE MPD A 304
04
AC4
SOFTWARE
HOH B:762
BINDING SITE FOR RESIDUE MPD A 305
05
AC5
SOFTWARE
PHE A:17 , VAL A:216
BINDING SITE FOR RESIDUE MPD A 306
06
AC6
SOFTWARE
ASP A:251 , HOH A:491 , HOH A:560 , HOH A:929 , ASN B:42 , ALA B:48
BINDING SITE FOR RESIDUE MRD A 307
07
AC7
SOFTWARE
GLN A:189 , HIS A:243 , CYS A:244
BINDING SITE FOR RESIDUE K A 308
08
AC8
SOFTWARE
ASN B:113 , TYR B:137 , GLY B:141 , ASP B:145 , ASN B:174 , LEU B:175 , ASN B:178 , HIS B:180
BINDING SITE FOR RESIDUE NAG B 302
09
AC9
SOFTWARE
LEU B:110 , ASN B:134 , ASN B:138 , HOH B:757 , HOH B:942 , HOH B:1342 , HOH B:1503 , HOH B:1775
BINDING SITE FOR RESIDUE NAG B 303
10
BC1
SOFTWARE
HIS B:9 , HOH B:492
BINDING SITE FOR RESIDUE MPD B 304
11
BC2
SOFTWARE
GLN A:12 , HOH A:793 , HOH A:1008 , GLN B:12 , HOH B:325 , HOH B:869 , GLN C:12 , HOH C:359
BINDING SITE FOR RESIDUE MPD B 305
12
BC3
SOFTWARE
ARG B:228 , ASP B:251 , HOH B:753 , HOH B:1327 , ASN C:42 , ALA C:48 , PRO C:51
BINDING SITE FOR RESIDUE MRD B 306
13
BC4
SOFTWARE
GLN B:189 , HIS B:243 , CYS B:244 , HOH B:371
BINDING SITE FOR RESIDUE K B 307
14
BC5
SOFTWARE
ARG A:99 , TRP A:238 , HOH A:1936 , ASN C:113 , TYR C:137 , GLY C:141 , ASP C:145 , ASN C:174 , LEU C:175 , ASN C:178 , HIS C:180 , HOH C:944 , HOH C:1730
BINDING SITE FOR RESIDUE NAG C 302
15
BC6
SOFTWARE
LEU C:110 , ALA C:112 , ASN C:134 , ASN C:138 , HOH C:546 , HOH C:860 , HOH C:970 , HOH C:1491 , HOH C:1623
BINDING SITE FOR RESIDUE NAG C 303
16
BC7
SOFTWARE
ASN A:42 , ALA A:48 , PRO A:51 , ARG C:228 , ASP C:251 , HOH C:469 , HOH C:1136
BINDING SITE FOR RESIDUE MPD C 304
17
BC8
SOFTWARE
HOH A:812 , HIS C:9 , HOH C:1774
BINDING SITE FOR RESIDUE MPD C 305
18
BC9
SOFTWARE
HOH C:329 , PHE D:38 , GLU E:54 , ILE E:56
BINDING SITE FOR RESIDUE MPD C 306
19
CC1
SOFTWARE
GLN C:189 , HIS C:243 , CYS C:244 , HOH C:333
BINDING SITE FOR RESIDUE K C 307
20
CC2
SOFTWARE
GLN B:102 , TRP B:238 , ASP B:239 , ASN D:113 , TYR D:137 , GLY D:141 , ASP D:145 , ASN D:174 , LEU D:175 , ASN D:178 , HIS D:180
BINDING SITE FOR RESIDUE NAG D 302
21
CC3
SOFTWARE
LEU D:110 , ILE D:130 , ASN D:134 , ASN D:138
BINDING SITE FOR RESIDUE NAG D 303
22
CC4
SOFTWARE
GLN D:12 , HOH D:326 , GLN E:12 , HOH E:367 , HOH E:503 , HOH E:1439 , GLN F:12 , HOH F:322
BINDING SITE FOR RESIDUE MPD D 304
23
CC5
SOFTWARE
ILE C:286 , GLY C:297 , HOH C:1379 , LEU D:91 , GLU D:92 , HOH D:930 , HOH D:959
BINDING SITE FOR RESIDUE MRD D 305
24
CC6
SOFTWARE
HIS D:9 , HOH E:561
BINDING SITE FOR RESIDUE MPD D 306
25
CC7
SOFTWARE
GLN D:189 , HIS D:243 , CYS D:244 , HOH D:444
BINDING SITE FOR RESIDUE K D 307
26
CC8
SOFTWARE
GLN C:102 , TRP C:238 , ASP C:239 , ASN E:113 , TYR E:137 , GLY E:141 , ASP E:145 , ASN E:174 , LEU E:175 , ASN E:178 , HIS E:180 , HOH E:994
BINDING SITE FOR RESIDUE NAG E 302
27
CC9
SOFTWARE
MET C:101 , HOH C:1443 , LEU E:110 , ALA E:112 , ILE E:130 , ASN E:134 , ASN E:138
BINDING SITE FOR RESIDUE NAG E 303
28
DC1
SOFTWARE
GLY B:297 , HOH B:1190 , HOH B:1367 , HOH B:1375 , HOH E:395 , HOH E:847 , HOH E:952
BINDING SITE FOR RESIDUE MPD E 304
29
DC2
SOFTWARE
HOH F:695
BINDING SITE FOR RESIDUE MPD E 305
30
DC3
SOFTWARE
GLN E:189 , HIS E:243 , CYS E:244 , HOH E:541
BINDING SITE FOR RESIDUE K E 306
31
DC4
SOFTWARE
ASN F:113 , TYR F:137 , GLY F:141 , ASP F:145 , ASN F:174 , LEU F:175 , ASN F:178 , HIS F:180
BINDING SITE FOR RESIDUE NAG F 302
32
DC5
SOFTWARE
GLN B:208 , ASP B:212 , HOH B:356 , LEU F:110 , ASN F:134 , ASN F:138
BINDING SITE FOR RESIDUE NAG F 303
33
DC6
SOFTWARE
HOH D:633 , HIS F:9
BINDING SITE FOR RESIDUE MRD F 304
34
DC7
SOFTWARE
HOH A:1117 , ILE F:286 , GLY F:297 , HOH F:339 , HOH F:1169 , HOH F:1305
BINDING SITE FOR RESIDUE MPD F 305
35
DC8
SOFTWARE
GLN F:189 , HIS F:243 , CYS F:244 , HOH F:470
BINDING SITE FOR RESIDUE K F 306
36
DC9
SOFTWARE
ASN G:113 , TYR G:137 , GLY G:141 , ASP G:145 , ASN G:174 , LEU G:175 , ASN G:178 , HIS G:180
BINDING SITE FOR RESIDUE NAG G 302
37
EC1
SOFTWARE
GLN E:102 , LEU G:110 , ILE G:130 , ASN G:134
BINDING SITE FOR RESIDUE NAG G 303
38
EC2
SOFTWARE
GLN G:189 , HIS G:243 , CYS G:244 , HOH G:1277
BINDING SITE FOR RESIDUE K G 304
[
close Site info
]
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 7)
Info
All SCOP Domains
1a: SCOP_d3o0da_ (A:)
1b: SCOP_d3o0db_ (B:)
1c: SCOP_d3o0dc_ (C:)
1d: SCOP_d3o0dd_ (D:)
1e: SCOP_d3o0de_ (E:)
1f: SCOP_d3o0df_ (F:)
1g: SCOP_d3o0dg_ (G:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
alpha/beta-Hydrolases
(971)
Superfamily
:
alpha/beta-Hydrolases
(971)
Family
:
automated matches
(184)
Protein domain
:
automated matches
(184)
Yarrowia lipolytica [TaxId: 4952]
(2)
1a
d3o0da_
A:
1b
d3o0db_
B:
1c
d3o0dc_
C:
1d
d3o0dd_
D:
1e
d3o0de_
E:
1f
d3o0df_
F:
1g
d3o0dg_
G:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
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Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(2, 14)
Info
all PFAM domains
1a: PFAM_Lipase_3_3o0dG01 (G:82-240)
1b: PFAM_Lipase_3_3o0dG02 (G:82-240)
1c: PFAM_Lipase_3_3o0dG03 (G:82-240)
1d: PFAM_Lipase_3_3o0dG04 (G:82-240)
1e: PFAM_Lipase_3_3o0dG05 (G:82-240)
1f: PFAM_Lipase_3_3o0dG06 (G:82-240)
1g: PFAM_Lipase_3_3o0dG07 (G:82-240)
2a: PFAM_Lipase3_N_3o0dG08 (G:1-58)
2b: PFAM_Lipase3_N_3o0dG09 (G:1-58)
2c: PFAM_Lipase3_N_3o0dG10 (G:1-58)
2d: PFAM_Lipase3_N_3o0dG11 (G:1-58)
2e: PFAM_Lipase3_N_3o0dG12 (G:1-58)
2f: PFAM_Lipase3_N_3o0dG13 (G:1-58)
2g: PFAM_Lipase3_N_3o0dG14 (G:1-58)
View:
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
AB_hydrolase
(347)
Family
:
Lipase_3
(11)
Yarrowia lipolytica (Candida lipolytica)
(1)
1a
Lipase_3-3o0dG01
G:82-240
1b
Lipase_3-3o0dG02
G:82-240
1c
Lipase_3-3o0dG03
G:82-240
1d
Lipase_3-3o0dG04
G:82-240
1e
Lipase_3-3o0dG05
G:82-240
1f
Lipase_3-3o0dG06
G:82-240
1g
Lipase_3-3o0dG07
G:82-240
Clan
:
no clan defined [family: Lipase3_N]
(2)
Family
:
Lipase3_N
(2)
Yarrowia lipolytica (Candida lipolytica)
(1)
2a
Lipase3_N-3o0dG08
G:1-58
2b
Lipase3_N-3o0dG09
G:1-58
2c
Lipase3_N-3o0dG10
G:1-58
2d
Lipase3_N-3o0dG11
G:1-58
2e
Lipase3_N-3o0dG12
G:1-58
2f
Lipase3_N-3o0dG13
G:1-58
2g
Lipase3_N-3o0dG14
G:1-58
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