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1JKU
Asym. Unit
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Asym.Unit (279 KB)
Biol.Unit 1 (270 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MANGANESE CATALASE FROM LACTOBACILLUS PLANTARUM
Authors
:
V. V. Barynin, M. M. Whittaker, S. V. Antonyuk, V. S. Lamzin, P. M. Harrison, P. J. Artymiuk, J. W. Whittaker
Date
:
13 Jul 01 (Deposition) - 13 Jul 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.84
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Hexamer, Catalase Dimanganese, Metalloenzyme, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. V. Barynin, M. M. Whittaker, S. V. Antonyuk, V. S. Lamzin, P. M. Harrison, P. J. Artymiuk, J. W. Whittaker
Crystal Structure Of Manganese Catalase From Lactobacillus Plantarum.
Structure V. 9 725 2001
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(3, 36)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: MANGANESE (III) ION (MN3a)
2b: MANGANESE (III) ION (MN3b)
2c: MANGANESE (III) ION (MN3c)
2d: MANGANESE (III) ION (MN3d)
2e: MANGANESE (III) ION (MN3e)
2f: MANGANESE (III) ION (MN3f)
2g: MANGANESE (III) ION (MN3g)
2h: MANGANESE (III) ION (MN3h)
2i: MANGANESE (III) ION (MN3i)
2j: MANGANESE (III) ION (MN3j)
2k: MANGANESE (III) ION (MN3k)
2l: MANGANESE (III) ION (MN3l)
3a: HYDROXIDE ION (OHa)
3b: HYDROXIDE ION (OHb)
3c: HYDROXIDE ION (OHc)
3d: HYDROXIDE ION (OHd)
3e: HYDROXIDE ION (OHe)
3f: HYDROXIDE ION (OHf)
3g: HYDROXIDE ION (OHg)
3h: HYDROXIDE ION (OHh)
3i: HYDROXIDE ION (OHi)
3j: HYDROXIDE ION (OHj)
3k: HYDROXIDE ION (OHk)
3l: HYDROXIDE ION (OHl)
3m: HYDROXIDE ION (OHm)
3n: HYDROXIDE ION (OHn)
3o: HYDROXIDE ION (OHo)
3p: HYDROXIDE ION (OHp)
3q: HYDROXIDE ION (OHq)
3r: HYDROXIDE ION (OHr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
6
Ligand/Ion
CALCIUM ION
2
MN3
12
Ligand/Ion
MANGANESE (III) ION
3
OH
18
Ligand/Ion
HYDROXIDE ION
[
close Hetero Component info
]
Sites
(36, 36)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:57 , ASP A:61 , ASN F:218 , SER F:220 , GLY F:222
BINDING SITE FOR RESIDUE CA A 1272
02
AC2
SOFTWARE
ASP B:57 , ASP B:61 , ASN C:218 , SER C:220 , GLY C:222 , HOH C:3332
BINDING SITE FOR RESIDUE CA B 2272
03
AC3
SOFTWARE
ASN B:218 , SER B:220 , GLY B:222 , ASP C:57 , ASP C:61
BINDING SITE FOR RESIDUE CA C 3272
04
AC4
SOFTWARE
ASP D:57 , ASP D:61 , ASN E:218 , SER E:220 , GLY E:222
BINDING SITE FOR RESIDUE CA D 4272
05
AC5
SOFTWARE
ASN D:218 , SER D:220 , GLY D:222 , SER D:225 , HOH D:4334 , ASP E:57 , ASP E:61
BINDING SITE FOR RESIDUE CA E 5272
06
AC6
SOFTWARE
ASN A:218 , SER A:220 , GLY A:222 , SER A:225 , ASP F:57 , ASP F:61
BINDING SITE FOR RESIDUE CA F 6272
07
AC7
SOFTWARE
GLU A:66 , HIS A:69 , HIS A:181 , MN3 A:1267 , MN3 A:1268 , OH A:1270 , OH A:1271
BINDING SITE FOR RESIDUE OH A 1269
08
AC8
SOFTWARE
GLU A:35 , GLU A:66 , ARG A:147 , GLU A:148 , GLU A:178 , MN3 A:1267 , MN3 A:1268 , OH A:1269 , OH A:1271
BINDING SITE FOR RESIDUE OH A 1270
09
AC9
SOFTWARE
GLU A:35 , HIS A:69 , LEU A:174 , GLU A:178 , MN3 A:1267 , OH A:1269 , OH A:1270
BINDING SITE FOR RESIDUE OH A 1271
10
BC1
SOFTWARE
GLU B:66 , HIS B:69 , HIS B:181 , MN3 B:2267 , MN3 B:2268 , OH B:2270 , OH B:2271
BINDING SITE FOR RESIDUE OH B 2269
11
BC2
SOFTWARE
GLU B:35 , GLU B:66 , ARG B:147 , GLU B:148 , GLU B:178 , MN3 B:2267 , MN3 B:2268 , OH B:2269 , OH B:2271
BINDING SITE FOR RESIDUE OH B 2270
12
BC3
SOFTWARE
GLU B:35 , HIS B:69 , LEU B:174 , GLU B:178 , MN3 B:2267 , OH B:2269 , OH B:2270
BINDING SITE FOR RESIDUE OH B 2271
13
BC4
SOFTWARE
GLU C:35 , GLU C:66 , HIS C:69 , HIS C:181 , MN3 C:3267 , MN3 C:3268 , OH C:3270 , OH C:3271
BINDING SITE FOR RESIDUE OH C 3269
14
BC5
SOFTWARE
GLU C:35 , GLU C:66 , ARG C:147 , GLU C:148 , GLU C:178 , MN3 C:3267 , MN3 C:3268 , OH C:3269 , OH C:3271
BINDING SITE FOR RESIDUE OH C 3270
15
BC6
SOFTWARE
GLU C:35 , HIS C:69 , LEU C:174 , GLU C:178 , MN3 C:3267 , OH C:3269 , OH C:3270
BINDING SITE FOR RESIDUE OH C 3271
16
BC7
SOFTWARE
GLU D:66 , HIS D:69 , GLU D:148 , HIS D:181 , MN3 D:4267 , MN3 D:4268 , OH D:4270 , OH D:4271
BINDING SITE FOR RESIDUE OH D 4269
17
BC8
SOFTWARE
GLU D:35 , GLU D:66 , ARG D:147 , GLU D:148 , GLU D:178 , MN3 D:4267 , MN3 D:4268 , OH D:4269 , OH D:4271
BINDING SITE FOR RESIDUE OH D 4270
18
BC9
SOFTWARE
GLU D:35 , HIS D:69 , LEU D:174 , GLU D:178 , MN3 D:4267 , OH D:4269 , OH D:4270
BINDING SITE FOR RESIDUE OH D 4271
19
CC1
SOFTWARE
GLU E:66 , HIS E:69 , HIS E:181 , MN3 E:5267 , MN3 E:5268 , OH E:5270 , OH E:5271
BINDING SITE FOR RESIDUE OH E 5269
20
CC2
SOFTWARE
GLU E:35 , GLU E:66 , ARG E:147 , GLU E:148 , GLU E:178 , MN3 E:5267 , MN3 E:5268 , OH E:5269 , OH E:5271
BINDING SITE FOR RESIDUE OH E 5270
21
CC3
SOFTWARE
GLU E:35 , HIS E:69 , LEU E:174 , GLU E:178 , MN3 E:5267 , OH E:5269 , OH E:5270
BINDING SITE FOR RESIDUE OH E 5271
22
CC4
SOFTWARE
GLU F:66 , HIS F:69 , HIS F:181 , MN3 F:6267 , MN3 F:6268 , OH F:6270 , OH F:6271
BINDING SITE FOR RESIDUE OH F 6269
23
CC5
SOFTWARE
GLU F:35 , GLU F:66 , ARG F:147 , GLU F:148 , GLU F:178 , MN3 F:6267 , MN3 F:6268 , OH F:6269 , OH F:6271
BINDING SITE FOR RESIDUE OH F 6270
24
CC6
SOFTWARE
GLU F:35 , HIS F:69 , LEU F:174 , GLU F:178 , MN3 F:6267 , OH F:6269 , OH F:6270
BINDING SITE FOR RESIDUE OH F 6271
25
CC7
SOFTWARE
GLU A:35 , GLU A:66 , HIS A:69 , MN3 A:1268 , OH A:1269 , OH A:1270 , OH A:1271
BINDING SITE FOR RESIDUE MN3 A 1267
26
CC8
SOFTWARE
GLU A:66 , ARG A:147 , GLU A:148 , HIS A:181 , MN3 A:1267 , OH A:1269 , OH A:1270
BINDING SITE FOR RESIDUE MN3 A 1268
27
CC9
SOFTWARE
GLU B:35 , GLU B:66 , HIS B:69 , MN3 B:2268 , OH B:2269 , OH B:2270 , OH B:2271
BINDING SITE FOR RESIDUE MN3 B 2267
28
DC1
SOFTWARE
GLU B:66 , ARG B:147 , GLU B:148 , HIS B:181 , MN3 B:2267 , OH B:2269 , OH B:2270
BINDING SITE FOR RESIDUE MN3 B 2268
29
DC2
SOFTWARE
GLU C:35 , GLU C:66 , HIS C:69 , MN3 C:3268 , OH C:3269 , OH C:3270 , OH C:3271
BINDING SITE FOR RESIDUE MN3 C 3267
30
DC3
SOFTWARE
GLU C:66 , ARG C:147 , GLU C:148 , HIS C:181 , MN3 C:3267 , OH C:3269 , OH C:3270
BINDING SITE FOR RESIDUE MN3 C 3268
31
DC4
SOFTWARE
GLU D:35 , GLU D:66 , HIS D:69 , MN3 D:4268 , OH D:4269 , OH D:4270 , OH D:4271
BINDING SITE FOR RESIDUE MN3 D 4267
32
DC5
SOFTWARE
GLU D:66 , ARG D:147 , GLU D:148 , HIS D:181 , MN3 D:4267 , OH D:4269 , OH D:4270
BINDING SITE FOR RESIDUE MN3 D 4268
33
DC6
SOFTWARE
GLU E:35 , GLU E:66 , HIS E:69 , MN3 E:5268 , OH E:5269 , OH E:5270 , OH E:5271
BINDING SITE FOR RESIDUE MN3 E 5267
34
DC7
SOFTWARE
GLU E:66 , ARG E:147 , GLU E:148 , HIS E:181 , MN3 E:5267 , OH E:5269 , OH E:5270
BINDING SITE FOR RESIDUE MN3 E 5268
35
DC8
SOFTWARE
GLU F:35 , GLU F:66 , HIS F:69 , MN3 F:6268 , OH F:6269 , OH F:6270 , OH F:6271
BINDING SITE FOR RESIDUE MN3 F 6267
36
DC9
SOFTWARE
GLU F:66 , ARG F:147 , GLU F:148 , HIS F:181 , MN3 F:6267 , OH F:6269 , OH F:6270
BINDING SITE FOR RESIDUE MN3 F 6268
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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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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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_d1jkua_ (A:)
1b: SCOP_d1jkub_ (B:)
1c: SCOP_d1jkuc_ (C:)
1d: SCOP_d1jkud_ (D:)
1e: SCOP_d1jkue_ (E:)
1f: SCOP_d1jkuf_ (F:)
View:
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)
(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Manganese catalase (T-catalase)
(7)
Protein domain
:
Manganese catalase (T-catalase)
(4)
Lactobacillus plantarum [TaxId: 1590]
(3)
1a
d1jkua_
A:
1b
d1jkub_
B:
1c
d1jkuc_
C:
1d
d1jkud_
D:
1e
d1jkue_
E:
1f
d1jkuf_
F:
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1jkuA02 (A:204-266)
1b: CATH_1jkuE02 (E:204-266)
1c: CATH_1jkuF02 (F:204-266)
1d: CATH_1jkuB02 (B:204-266)
1e: CATH_1jkuC02 (C:204-266)
1f: CATH_1jkuD02 (D:204-266)
2a: CATH_1jkuA01 (A:1-203)
2b: CATH_1jkuE01 (E:1-203)
2c: CATH_1jkuF01 (F:1-203)
2d: CATH_1jkuB01 (B:1-203)
2e: CATH_1jkuC01 (C:1-203)
2f: CATH_1jkuD01 (D:1-203)
View:
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
manganese catalase, domain 2, chain A
(3)
Homologous Superfamily
:
manganese catalase, domain 2, chain A
(3)
Lactobacillus plantarum. Organism_taxid: 1590. Strain: atcc 14431.
(2)
1a
1jkuA02
A:204-266
1b
1jkuE02
E:204-266
1c
1jkuF02
F:204-266
1d
1jkuB02
B:204-266
1e
1jkuC02
C:204-266
1f
1jkuD02
D:204-266
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Ferritin;
(180)
Homologous Superfamily
:
[code=1.20.1260.10, no name defined]
(180)
Lactobacillus plantarum. Organism_taxid: 1590. Strain: atcc 14431.
(2)
2a
1jkuA01
A:1-203
2b
1jkuE01
E:1-203
2c
1jkuF01
F:1-203
2d
1jkuB01
B:1-203
2e
1jkuC01
C:1-203
2f
1jkuD01
D:1-203
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Atom Selection
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