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3PNZ
Asym. Unit
Info
Asym.Unit (361 KB)
Biol.Unit 1 (65 KB)
Biol.Unit 2 (64 KB)
Biol.Unit 3 (66 KB)
Biol.Unit 4 (65 KB)
Biol.Unit 5 (66 KB)
Biol.Unit 6 (66 KB)
Biol.Unit 7 (181 KB)
Biol.Unit 8 (179 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE LACTONASE LMO2620 FROM LISTERIA MONOCYTOGENES
Authors
:
A. A. Fedorov, E. V. Fedorov, D. F. Xiang, F. M. Raushel, S. C. Almo
Date
:
20 Nov 10 (Deposition) - 23 Nov 11 (Release) - 23 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B,C,D,E,F
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: A,C,F (1x)
Biol. Unit 8: B,D,E (1x)
Keywords
:
Amidohydrolase Fold, Hydrolysis Of Phosphorylated Sugar Lactones, Phosphorylated Sugar Lactones, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. A. Fedorov, E. V. Fedorov, D. F. Xiang, F. M. Raushel, S. C. Almo
Crystal Structure Of The Lactonase Lmo2620 From Listeria Monocytogenes
To Be Published
[
close entry info
]
Hetero Components
(4, 60)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
1l: GLYCEROL (GOLl)
1m: GLYCEROL (GOLm)
1n: GLYCEROL (GOLn)
1o: GLYCEROL (GOLo)
1p: GLYCEROL (GOLp)
1q: GLYCEROL (GOLq)
1r: GLYCEROL (GOLr)
1s: GLYCEROL (GOLs)
1t: GLYCEROL (GOLt)
1u: GLYCEROL (GOLu)
2a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
2b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
2c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
2d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
2e: LYSINE NZ-CARBOXYLIC ACID (KCXe)
2f: LYSINE NZ-CARBOXYLIC ACID (KCXf)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
3d: PHOSPHATE ION (PO4d)
3e: PHOSPHATE ION (PO4e)
3f: PHOSPHATE ION (PO4f)
3g: PHOSPHATE ION (PO4g)
3h: PHOSPHATE ION (PO4h)
3i: PHOSPHATE ION (PO4i)
3j: PHOSPHATE ION (PO4j)
3k: PHOSPHATE ION (PO4k)
3l: PHOSPHATE ION (PO4l)
3m: PHOSPHATE ION (PO4m)
3n: PHOSPHATE ION (PO4n)
3o: PHOSPHATE ION (PO4o)
3p: PHOSPHATE ION (PO4p)
3q: PHOSPHATE ION (PO4q)
3r: PHOSPHATE ION (PO4r)
3s: PHOSPHATE ION (PO4s)
3t: PHOSPHATE ION (PO4t)
3u: PHOSPHATE ION (PO4u)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
4f: ZINC ION (ZNf)
4g: ZINC ION (ZNg)
4h: ZINC ION (ZNh)
4i: ZINC ION (ZNi)
4j: ZINC ION (ZNj)
4k: ZINC ION (ZNk)
4l: ZINC ION (ZNl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
21
Ligand/Ion
GLYCEROL
2
KCX
6
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
3
PO4
21
Ligand/Ion
PHOSPHATE ION
4
ZN
12
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(54, 54)
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)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (SOFTWARE)
54: FC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO C:207 , LEU C:208 , GLU C:209 , THR C:231 , HOH C:1498
BINDING SITE FOR RESIDUE GOL C 331
02
AC2
SOFTWARE
TYR D:8 , TYR D:148
BINDING SITE FOR RESIDUE GOL D 331
03
AC3
SOFTWARE
GLU B:209 , ARG B:324 , THR B:327 , LYS B:329 , HOH B:1532
BINDING SITE FOR RESIDUE GOL B 331
04
AC4
SOFTWARE
TYR F:8 , SER F:82 , GLY F:86 , GLN F:88 , HOH F:605 , HOH F:864
BINDING SITE FOR RESIDUE GOL F 331
05
AC5
SOFTWARE
HOH A:498 , ILE C:240 , ALA C:241 , GLY C:271 , THR C:273 , TYR C:278 , GLY C:287 , HOH C:730
BINDING SITE FOR RESIDUE GOL C 332
06
AC6
SOFTWARE
HOH B:589 , ILE E:240 , ALA E:241 , GLY E:271 , THR E:273 , TYR E:278 , GLY E:287 , HOH E:977
BINDING SITE FOR RESIDUE GOL E 331
07
AC7
SOFTWARE
ILE D:240 , ALA D:241 , GLY D:271 , THR D:273 , TYR D:278 , GLY D:287 , HOH D:379 , HOH D:571
BINDING SITE FOR RESIDUE GOL D 332
08
AC8
SOFTWARE
GLY F:271 , THR F:273 , TYR F:278 , PRO F:286 , GLY F:287 , HOH F:386 , HOH F:518
BINDING SITE FOR RESIDUE GOL F 332
09
AC9
SOFTWARE
ASP E:43 , ARG E:74 , ASP E:77 , HOH E:579
BINDING SITE FOR RESIDUE GOL E 332
10
BC1
SOFTWARE
PHE C:18 , LEU C:58 , ALA C:292 , HOH C:1191
BINDING SITE FOR RESIDUE GOL C 333
11
BC2
SOFTWARE
LYS E:226 , LYS E:230 , HOH E:834 , HOH E:930 , HOH E:1503
BINDING SITE FOR RESIDUE GOL E 333
12
BC3
SOFTWARE
GLU C:189
BINDING SITE FOR RESIDUE GOL C 334
13
BC4
SOFTWARE
LEU A:58 , ALA A:292 , HOH A:953
BINDING SITE FOR RESIDUE GOL A 331
14
BC5
SOFTWARE
ILE E:198 , LYS E:202 , HOH E:393 , HOH E:395
BINDING SITE FOR RESIDUE GOL E 334
15
BC6
SOFTWARE
LYS C:226 , LYS C:230 , HOH C:822 , HOH C:995 , HOH C:1270
BINDING SITE FOR RESIDUE GOL C 335
16
BC7
SOFTWARE
PHE B:18 , LEU B:58 , GLY B:59 , ALA B:292 , HOH B:908
BINDING SITE FOR RESIDUE GOL B 332
17
BC8
SOFTWARE
LYS C:312 , LYS C:316
BINDING SITE FOR RESIDUE GOL C 336
18
BC9
SOFTWARE
PHE F:18 , LEU F:58 , ALA F:292 , HOH F:1440
BINDING SITE FOR RESIDUE GOL F 333
19
CC1
SOFTWARE
TYR B:223 , LYS B:226 , GLN B:227 , LYS B:230 , HOH B:978
BINDING SITE FOR RESIDUE GOL B 333
20
CC2
SOFTWARE
GLU A:209 , ARG A:324 , LYS A:329 , HOH A:691 , PRO E:147 , TYR E:148 , HOH E:1495
BINDING SITE FOR RESIDUE GOL A 332
21
CC3
SOFTWARE
TYR D:8 , SER D:82 , LYS D:83 , GLY D:86 , ILE D:87 , GLN D:88 , HOH D:598 , HOH D:896 , HOH D:1193 , HOH D:1467
BINDING SITE FOR RESIDUE GOL D 333
22
CC4
SOFTWARE
HIS A:22 , HIS A:24 , KCX A:154 , ASP A:272 , PO4 A:335
BINDING SITE FOR RESIDUE ZN A 333
23
CC5
SOFTWARE
HIS B:22 , HIS B:24 , KCX B:154 , ASP B:272 , PO4 B:336
BINDING SITE FOR RESIDUE ZN B 334
24
CC6
SOFTWARE
HIS C:22 , HIS C:24 , KCX C:154 , ASP C:272 , PO4 C:339
BINDING SITE FOR RESIDUE ZN C 337
25
CC7
SOFTWARE
HIS D:22 , HIS D:24 , KCX D:154 , ASP D:272 , PO4 D:336
BINDING SITE FOR RESIDUE ZN D 334
26
CC8
SOFTWARE
HIS E:22 , HIS E:24 , KCX E:154 , ASP E:272 , PO4 E:337
BINDING SITE FOR RESIDUE ZN E 335
27
CC9
SOFTWARE
HIS F:22 , HIS F:24 , KCX F:154 , ASP F:272 , PO4 F:336
BINDING SITE FOR RESIDUE ZN F 334
28
DC1
SOFTWARE
ASN A:96 , KCX A:154 , HIS A:187 , HIS A:215 , PO4 A:335
BINDING SITE FOR RESIDUE ZN A 334
29
DC2
SOFTWARE
ASN B:96 , KCX B:154 , HIS B:187 , HIS B:215 , PO4 B:336
BINDING SITE FOR RESIDUE ZN B 335
30
DC3
SOFTWARE
KCX C:154 , HIS C:187 , HIS C:215 , PO4 C:339
BINDING SITE FOR RESIDUE ZN C 338
31
DC4
SOFTWARE
KCX D:154 , HIS D:187 , HIS D:215 , PO4 D:336
BINDING SITE FOR RESIDUE ZN D 335
32
DC5
SOFTWARE
KCX E:154 , HIS E:187 , HIS E:215 , PO4 E:337
BINDING SITE FOR RESIDUE ZN E 336
33
DC6
SOFTWARE
KCX F:154 , HIS F:187 , HIS F:215 , PO4 F:336
BINDING SITE FOR RESIDUE ZN F 335
34
DC7
SOFTWARE
HIS A:22 , HIS A:24 , TYR A:71 , ASN A:96 , LYS A:97 , KCX A:154 , HIS A:187 , HIS A:215 , ASP A:272 , ZN A:333 , ZN A:334
BINDING SITE FOR RESIDUE PO4 A 335
35
DC8
SOFTWARE
HIS B:22 , HIS B:24 , TYR B:71 , ASN B:96 , LYS B:97 , KCX B:154 , HIS B:187 , HIS B:215 , ASP B:272 , ZN B:334 , ZN B:335
BINDING SITE FOR RESIDUE PO4 B 336
36
DC9
SOFTWARE
HIS C:22 , HIS C:24 , TYR C:71 , ASN C:96 , LYS C:97 , KCX C:154 , HIS C:187 , HIS C:215 , ASP C:272 , ZN C:337 , ZN C:338 , HOH C:974 , HOH C:1550
BINDING SITE FOR RESIDUE PO4 C 339
37
EC1
SOFTWARE
HIS D:22 , HIS D:24 , ASN D:96 , LYS D:97 , KCX D:154 , HIS D:187 , HIS D:215 , ASP D:272 , ZN D:334 , ZN D:335 , HOH D:1139
BINDING SITE FOR RESIDUE PO4 D 336
38
EC2
SOFTWARE
HIS E:22 , HIS E:24 , TYR E:71 , ASN E:96 , LYS E:97 , KCX E:154 , HIS E:187 , HIS E:215 , ASP E:272 , ZN E:335 , ZN E:336 , HOH E:1012 , HOH E:1548
BINDING SITE FOR RESIDUE PO4 E 337
39
EC3
SOFTWARE
HIS F:22 , HIS F:24 , TYR F:71 , ASN F:96 , LYS F:97 , KCX F:154 , HIS F:187 , HIS F:215 , ASP F:272 , ZN F:334 , ZN F:335 , HOH F:968
BINDING SITE FOR RESIDUE PO4 F 336
40
EC4
SOFTWARE
LYS A:242 , LYS A:244 , TYR A:245 , ARG A:275 , TYR A:278 , HOH A:1049 , HOH A:1102 , HOH A:1143
BINDING SITE FOR RESIDUE PO4 A 336
41
EC5
SOFTWARE
LYS B:242 , LYS B:244 , TYR B:245 , ARG B:275 , TYR B:278 , HOH B:1071 , HOH B:1105 , HOH B:1333
BINDING SITE FOR RESIDUE PO4 B 337
42
EC6
SOFTWARE
LYS C:242 , LYS C:244 , TYR C:245 , ARG C:275 , TYR C:278 , HOH C:809 , HOH C:951 , HOH C:974 , HOH C:1103
BINDING SITE FOR RESIDUE PO4 C 340
43
EC7
SOFTWARE
LYS D:242 , LYS D:244 , TYR D:245 , ARG D:275 , TYR D:278 , HOH D:935 , HOH D:1139
BINDING SITE FOR RESIDUE PO4 D 337
44
EC8
SOFTWARE
LYS E:242 , LYS E:244 , TYR E:245 , ARG E:275 , TYR E:278 , HOH E:980 , HOH E:990 , HOH E:1012 , HOH E:1500
BINDING SITE FOR RESIDUE PO4 E 338
45
EC9
SOFTWARE
LYS F:242 , LYS F:244 , TYR F:245 , ARG F:275 , TYR F:278 , HOH F:898 , HOH F:968 , HOH F:1055 , HOH F:1428
BINDING SITE FOR RESIDUE PO4 F 337
46
FC1
SOFTWARE
THR D:127 , THR D:128 , HOH D:1014
BINDING SITE FOR RESIDUE PO4 D 338
47
FC2
SOFTWARE
THR C:127 , THR C:128 , HOH C:714
BINDING SITE FOR RESIDUE PO4 C 341
48
FC3
SOFTWARE
THR E:127 , THR E:128 , HOH E:773
BINDING SITE FOR RESIDUE PO4 E 339
49
FC4
SOFTWARE
THR B:128 , LYS B:168 , HOH B:1509 , HOH B:1539
BINDING SITE FOR RESIDUE PO4 B 338
50
FC5
SOFTWARE
THR F:127 , THR F:128 , HOH F:945 , HOH F:1520
BINDING SITE FOR RESIDUE PO4 F 338
51
FC6
SOFTWARE
THR A:127 , THR A:128 , HOH A:1513
BINDING SITE FOR RESIDUE PO4 A 337
52
FC7
SOFTWARE
SER E:82 , GLY E:86 , GLN E:88 , HOH E:356 , HOH E:421 , HOH E:928
BINDING SITE FOR RESIDUE PO4 E 340
53
FC8
SOFTWARE
LYS E:312 , LYS E:316 , HOH E:933
BINDING SITE FOR RESIDUE PO4 E 341
54
FC9
SOFTWARE
SER C:82 , GLY C:86 , ILE C:87 , HOH C:419 , HOH C:916 , HOH C:1371
BINDING SITE FOR RESIDUE PO4 C 342
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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Label:
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, 6)
Info
All SCOP Domains
1a: SCOP_d3pnza_ (A:)
1b: SCOP_d3pnzb_ (B:)
1c: SCOP_d3pnzc_ (C:)
1d: SCOP_d3pnzd_ (D:)
1e: SCOP_d3pnze_ (E:)
1f: SCOP_d3pnzf_ (F:)
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
automated matches
(44)
Protein domain
:
automated matches
(44)
Listeria monocytogenes [TaxId: 267410]
(1)
1a
d3pnza_
A:
1b
d3pnzb_
B:
1c
d3pnzc_
C:
1d
d3pnzd_
D:
1e
d3pnze_
E:
1f
d3pnzf_
F:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
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