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2Q9O
Biol. Unit 1
Info
Asym.Unit (440 KB)
Biol.Unit 1 (414 KB)
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(1)
Title
:
NEAR-ATOMIC RESOLUTION STRUCTURE OF A MELANOCARPUS ALBOMYCES LACCASE
Authors
:
N. Hakulinen, J. Rouvinen
Date
:
13 Jun 07 (Deposition) - 25 Mar 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.30
Chains
:
Asym. Unit : A,B,C
#
,D
#
,E
#
,G
#
,H
#
,I
#
,J
#
,K
#
,L
#
Biol. Unit 1: A,B (1x)
(
#
: chains that contain no standard or modified protein/DNA/RNA residue)
Keywords
:
Laccase, Multicopper Oxidase, Melanocarpus Albomyces, 2-Oxohistidine, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Hakulinen, M. Andberg, J. Kallio, A. Koivula, K. Kruus, J. Rouvinen
A Near Atomic Resolution Structure Of A Melanocarpus Albomyces Laccase.
J. Struct. Biol. V. 162 29 2008
[
close entry info
]
Hetero Components
(5, 18)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: COPPER (II) ION (CUa)
2b: COPPER (II) ION (CUb)
2c: COPPER (II) ION (CUc)
2d: COPPER (II) ION (CUd)
2e: COPPER (II) ION (CUe)
2f: COPPER (II) ION (CUf)
2g: COPPER (II) ION (CUg)
2h: COPPER (II) ION (CUh)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
4d: ALPHA-D-MANNOSE (MANd)
4e: ALPHA-D-MANNOSE (MANe)
4f: ALPHA-D-MANNOSE (MANf)
4g: ALPHA-D-MANNOSE (MANg)
4h: ALPHA-D-MANNOSE (MANh)
4i: ALPHA-D-MANNOSE (MANi)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
5i: N-ACETYL-D-GLUCOSAMINE (NAGi)
5j: N-ACETYL-D-GLUCOSAMINE (NAGj)
5k: N-ACETYL-D-GLUCOSAMINE (NAGk)
5l: N-ACETYL-D-GLUCOSAMINE (NAGl)
5m: N-ACETYL-D-GLUCOSAMINE (NAGm)
5n: N-ACETYL-D-GLUCOSAMINE (NAGn)
5o: N-ACETYL-D-GLUCOSAMINE (NAGo)
5p: N-ACETYL-D-GLUCOSAMINE (NAGp)
5q: N-ACETYL-D-GLUCOSAMINE (NAGq)
5r: N-ACETYL-D-GLUCOSAMINE (NAGr)
5s: N-ACETYL-D-GLUCOSAMINE (NAGs)
5t: N-ACETYL-D-GLUCOSAMINE (NAGt)
5u: N-ACETYL-D-GLUCOSAMINE (NAGu)
5v: N-ACETYL-D-GLUCOSAMINE (NAGv)
5w: N-ACETYL-D-GLUCOSAMINE (NAGw)
5x: N-ACETYL-D-GLUCOSAMINE (NAGx)
5y: N-ACETYL-D-GLUCOSAMINE (NAGy)
6a: 3-(2-OXO-2H-IMIDAZOL-4-YL)-L-ALANI... (OHIa)
6b: 3-(2-OXO-2H-IMIDAZOL-4-YL)-L-ALANI... (OHIb)
7a: OXYGEN MOLECULE (OXYa)
7b: OXYGEN MOLECULE (OXYb)
8a: SULFATE ION (SO4a)
8b: SULFATE ION (SO4b)
8c: SULFATE ION (SO4c)
8d: SULFATE ION (SO4d)
8e: SULFATE ION (SO4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
CU
-1
Ligand/Ion
COPPER (II) ION
3
GOL
2
Ligand/Ion
GLYCEROL
4
MAN
-1
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
OHI
2
Mod. Amino Acid
3-(2-OXO-2H-IMIDAZOL-4-YL)-L-ALANINE
7
OXY
2
Ligand/Ion
OXYGEN MOLECULE
8
SO4
5
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(49, 49)
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: AC9 (SOFTWARE)
09: BC1 (SOFTWARE)
10: BC2 (SOFTWARE)
11: BC3 (SOFTWARE)
12: BC4 (SOFTWARE)
13: BC6 (SOFTWARE)
14: BC7 (SOFTWARE)
15: BC8 (SOFTWARE)
16: BC9 (SOFTWARE)
17: CC1 (SOFTWARE)
18: CC2 (SOFTWARE)
19: CC3 (SOFTWARE)
20: CC4 (SOFTWARE)
21: CC5 (SOFTWARE)
22: CC6 (SOFTWARE)
23: CC7 (SOFTWARE)
24: CC8 (SOFTWARE)
25: CC9 (SOFTWARE)
26: DC1 (SOFTWARE)
27: DC2 (SOFTWARE)
28: DC3 (SOFTWARE)
29: DC5 (SOFTWARE)
30: DC6 (SOFTWARE)
31: DC7 (SOFTWARE)
32: DC8 (SOFTWARE)
33: DC9 (SOFTWARE)
34: EC1 (SOFTWARE)
35: EC2 (SOFTWARE)
36: EC3 (SOFTWARE)
37: EC4 (SOFTWARE)
38: EC5 (SOFTWARE)
39: EC6 (SOFTWARE)
40: EC7 (SOFTWARE)
41: EC8 (SOFTWARE)
42: EC9 (SOFTWARE)
43: FC1 (SOFTWARE)
44: FC2 (SOFTWARE)
45: FC3 (SOFTWARE)
46: FC4 (SOFTWARE)
47: FC5 (SOFTWARE)
48: FC6 (SOFTWARE)
49: FC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:39 , ASN A:84 , HOH A:4382 , HOH A:4407 , HOH A:4559 , GLU B:78 , ARG B:126 , HOH B:4675
BINDING SITE FOR RESIDUE NAG A 1001
02
AC2
SOFTWARE
LYS A:56 , MET A:58 , THR A:87 , ASN A:88 , ASP A:181 , ASN A:550 , TYR A:552 , HOH A:4041 , HOH A:4054 , HOH A:4146 , HOH A:4190 , HOH C:17
BINDING SITE FOR RESIDUE NAG C 11
03
AC3
SOFTWARE
GLU A:55 , ALA A:179 , ASP A:181 , ASP A:182 , TYR A:552 , HOH A:4011 , HOH A:4401 , HOH C:14 , HOH C:15 , HOH C:16
BINDING SITE FOR RESIDUE NAG C 12
04
AC4
SOFTWARE
ASN A:216 , THR A:218 , HIS A:311 , GLY A:317 , GLY A:318 , HOH D:23 , HOH D:24
BINDING SITE FOR RESIDUE NAG D 21
05
AC5
SOFTWARE
HIS A:311 , ALA A:313 , GLY A:314 , GLY A:317 , HOH A:4399
BINDING SITE FOR RESIDUE NAG D 22
06
AC6
SOFTWARE
TRP A:287 , ASN A:289 , THR A:291 , HIS A:305 , ALA A:307 , GLU A:323 , THR A:325 , HOH A:4168 , HOH E:35 , HOH E:37
BINDING SITE FOR RESIDUE NAG E 31
07
AC7
SOFTWARE
TYR A:214 , TRP A:287 , HIS A:305 , GLU A:323 , HOH E:34 , HOH E:38
BINDING SITE FOR RESIDUE NAG E 32
08
AC9
SOFTWARE
PRO A:355 , ASP A:356 , THR A:358 , LEU A:359 , ASN A:376 , HOH A:4414 , HOH A:4618
BINDING SITE FOR RESIDUE NAG A 1002
09
BC1
SOFTWARE
PRO A:355 , ASP A:356
BINDING SITE FOR RESIDUE NAG A 1003
10
BC2
SOFTWARE
LYS A:386 , TYR A:391 , ASN A:396 , SER A:398 , HOH A:4310 , HOH A:4520 , HOH A:4661 , GLN B:530
BINDING SITE FOR RESIDUE NAG A 1051
11
BC3
SOFTWARE
LEU A:167 , PHE A:170 , ASN A:201 , LEU A:227 , HOH G:73 , HOH G:76
BINDING SITE FOR RESIDUE NAG G 61
12
BC4
SOFTWARE
ASP A:166 , GLY A:168 , HOH G:67 , HOH G:68 , HOH G:70 , HOH G:77
BINDING SITE FOR RESIDUE NAG G 62
13
BC6
SOFTWARE
HOH A:4140 , HOH A:4528 , HOH G:74
BINDING SITE FOR RESIDUE MAN G 64
14
BC7
SOFTWARE
ARG A:10 , HOH G:66 , HOH G:69
BINDING SITE FOR RESIDUE MAN G 65
15
BC8
SOFTWARE
ASN A:244 , TYR A:286 , HOH A:4257 , HOH A:4403 , HOH A:4438 , ARG B:281 , HOH B:4275
BINDING SITE FOR RESIDUE NAG A 1071
16
BC9
SOFTWARE
GLU A:78 , ARG A:126 , ASN B:39 , ASN B:84 , HOH B:4488 , HOH B:4671
BINDING SITE FOR RESIDUE NAG B 1001
17
CC1
SOFTWARE
LYS B:56 , THR B:87 , ASN B:88 , ASP B:181 , ASN B:550 , TYR B:552 , HOH B:4033 , HOH B:4034 , HOH B:4138 , HOH H:1014 , HOH H:1018
BINDING SITE FOR RESIDUE NAG H 1011
18
CC2
SOFTWARE
GLU B:55 , ALA B:179 , ASP B:181 , ASP B:182 , HOH B:4058 , HOH H:1015 , HOH H:1016 , HOH H:1017
BINDING SITE FOR RESIDUE NAG H 1012
19
CC3
SOFTWARE
HIS B:185 , HOH H:1016 , HOH H:1020 , HOH H:1021
BINDING SITE FOR RESIDUE MAN H 1013
20
CC4
SOFTWARE
ASN B:216 , THR B:218 , ILE B:309 , HIS B:311 , GLY B:317 , GLY B:318 , HOH I:1023 , HOH I:1024
BINDING SITE FOR RESIDUE NAG I 1021
21
CC5
SOFTWARE
HIS B:311 , ALA B:313 , GLY B:314 , HOH B:4427
BINDING SITE FOR RESIDUE NAG I 1022
22
CC6
SOFTWARE
TRP B:287 , ASN B:289 , HIS B:305 , ALA B:307 , GLU B:323 , THR B:325 , HOH B:4142 , HOH J:1034
BINDING SITE FOR RESIDUE NAG J 1031
23
CC7
SOFTWARE
TYR B:214 , TRP B:287 , HIS B:305 , GLU B:323 , HOH J:1034
BINDING SITE FOR RESIDUE NAG J 1032
24
CC8
SOFTWARE
PRO B:355 , ASP B:356 , THR B:358 , LEU B:359 , ASN B:376 , HOH K:1043
BINDING SITE FOR RESIDUE NAG K 1041
25
CC9
SOFTWARE
PRO B:355 , HOH K:1044
BINDING SITE FOR RESIDUE NAG K 1042
26
DC1
SOFTWARE
ASP A:379 , ASN A:381 , HOH A:4581 , LYS B:386 , ASN B:396 , HOH B:4229 , HOH B:4497 , HOH B:4569 , HOH B:4685
BINDING SITE FOR RESIDUE NAG B 1051
27
DC2
SOFTWARE
LEU B:167 , ASN B:201 , LEU B:227 , HOH L:1073
BINDING SITE FOR RESIDUE NAG L 1061
28
DC3
SOFTWARE
ASP B:166 , HOH L:1067 , HOH L:1068 , HOH L:1070 , HOH L:1072
BINDING SITE FOR RESIDUE NAG L 1062
29
DC5
SOFTWARE
ASP B:166 , HOH L:1071
BINDING SITE FOR RESIDUE MAN L 1064
30
DC6
SOFTWARE
ARG B:10 , HOH B:4677 , HOH L:1066 , HOH L:1069 , HOH L:1077 , HOH L:1078
BINDING SITE FOR RESIDUE MAN L 1065
31
DC7
SOFTWARE
HIS A:431 , CYS A:503 , ILE A:505 , HIS A:508 , LEU A:513
BINDING SITE FOR RESIDUE CU A 2001
32
DC8
SOFTWARE
HIS A:140 , HIS A:436 , HIS A:502
BINDING SITE FOR RESIDUE CU A 2002
33
DC9
SOFTWARE
HIS A:95 , TRP A:136 , HIS A:138 , HIS A:504
BINDING SITE FOR RESIDUE CU A 2003
34
EC1
SOFTWARE
HIS A:93 , HIS A:95 , HIS A:434 , HIS A:436
BINDING SITE FOR RESIDUE CU A 2004
35
EC2
SOFTWARE
HIS A:93 , GLY A:96 , HIS A:434 , HOH A:4107
BINDING SITE FOR RESIDUE CL A 2010
36
EC3
SOFTWARE
HIS B:431 , CYS B:503 , ILE B:505 , HIS B:508
BINDING SITE FOR RESIDUE CU B 2001
37
EC4
SOFTWARE
HIS B:140 , HIS B:436 , HIS B:502
BINDING SITE FOR RESIDUE CU B 2002
38
EC5
SOFTWARE
HIS B:95 , TRP B:136 , HIS B:138 , HIS B:504
BINDING SITE FOR RESIDUE CU B 2003
39
EC6
SOFTWARE
HIS B:93 , HIS B:95 , HIS B:434 , HIS B:436
BINDING SITE FOR RESIDUE CU B 2004
40
EC7
SOFTWARE
HIS B:93 , GLY B:96 , HIS B:434 , HOH B:4160
BINDING SITE FOR RESIDUE CL B 2010
41
EC8
SOFTWARE
ARG A:492 , HOH A:4612 , HOH A:4621 , ARG B:128 , ARG B:130
BINDING SITE FOR RESIDUE SO4 A 4001
42
EC9
SOFTWARE
ARG A:128 , ARG A:130 , ARG B:492
BINDING SITE FOR RESIDUE SO4 B 4002
43
FC1
SOFTWARE
ARG A:520 , ARG A:527 , HOH A:4260 , HOH A:4461 , HOH A:4513 , HOH A:4605 , HOH A:4638 , HOH A:4654 , ARG B:520 , ARG B:527
BINDING SITE FOR RESIDUE SO4 A 4003
44
FC2
SOFTWARE
PRO B:447 , ASP B:448 , ARG B:467 , HOH B:4239 , HOH B:4445
BINDING SITE FOR RESIDUE SO4 B 4004
45
FC3
SOFTWARE
PRO A:447 , ASP A:448 , ARG A:467 , HOH A:4275 , HOH A:4664
BINDING SITE FOR RESIDUE SO4 A 4005
46
FC4
SOFTWARE
HIS A:93 , HIS A:95 , HIS A:138 , HIS A:140 , HIS A:434 , HIS A:436 , HIS A:502 , HIS A:504
BINDING SITE FOR RESIDUE OXY A 4006
47
FC5
SOFTWARE
HIS B:93 , HIS B:95 , HIS B:138 , HIS B:140 , HIS B:434 , HIS B:436 , HIS B:502 , HIS B:504
BINDING SITE FOR RESIDUE OXY B 4005
48
FC6
SOFTWARE
ALA A:191 , PRO A:192 , PHE A:371 , TRP A:373 , PHE A:427 , LEU A:429 , HOH A:4082 , HOH A:4093 , HOH A:4189
BINDING SITE FOR RESIDUE GOL A 3001
49
FC7
SOFTWARE
ALA B:191 , PRO B:192 , PHE B:371 , TRP B:373 , LEU B:429 , HOH B:4059 , HOH B:4089 , HOH B:4198
BINDING SITE FOR RESIDUE GOL B 3002
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: MULTICOPPER_OXIDASE1 (A:497-517,B:497-517)
2: MULTICOPPER_OXIDASE2 (A:502-513,B:502-513)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MULTICOPPER_OXIDASE1
PS00079
Multicopper oxidases signature 1.
LAC1_MELAO
547-567
2
A:497-517
B:497-517
2
MULTICOPPER_OXIDASE2
PS00080
Multicopper oxidases signature 2.
LAC1_MELAO
552-563
2
A:502-513
B:502-513
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d2q9oa1 (A:1-162)
1b: SCOP_d2q9oa2 (A:163-343)
1c: SCOP_d2q9oa3 (A:344-559)
1d: SCOP_d2q9ob1 (B:1-162)
1e: SCOP_d2q9ob2 (B:163-343)
1f: SCOP_d2q9ob3 (B:344-559)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Multidomain cupredoxins
(146)
Protein domain
:
Laccase
(13)
Fungus (Melanocarpus albomyces) [TaxId: 204285]
(8)
1a
d2q9oa1
A:1-162
1b
d2q9oa2
A:163-343
1c
d2q9oa3
A:344-559
1d
d2q9ob1
B:1-162
1e
d2q9ob2
B:163-343
1f
d2q9ob3
B:344-559
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_2q9oA01 (A:1-158)
1b: CATH_2q9oB01 (B:1-158)
1c: CATH_2q9oA02 (A:159-342)
1d: CATH_2q9oB02 (B:159-342)
1e: CATH_2q9oA03 (A:343-559)
1f: CATH_2q9oB03 (B:343-559)
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Topologies
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Homologous Superfamilies
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)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Melanocarpus albomyces. Organism_taxid: 204285. Strain: vtt d-96490.
(7)
1a
2q9oA01
A:1-158
1b
2q9oB01
B:1-158
1c
2q9oA02
A:159-342
1d
2q9oB02
B:159-342
1e
2q9oA03
A:343-559
1f
2q9oB03
B:343-559
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Cu_oxidase_2q9oB01 (B:166-315)
1b: PFAM_Cu_oxidase_2q9oB02 (B:166-315)
2a: PFAM_Cu_oxidase_2_2q9oB03 (B:359-523)
2b: PFAM_Cu_oxidase_2_2q9oB04 (B:359-523)
3a: PFAM_Cu_oxidase_3_2q9oB05 (B:41-160)
3b: PFAM_Cu_oxidase_3_2q9oB06 (B:41-160)
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Families
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Organisms
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(
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Clan
:
CU_oxidase
(192)
Family
:
Cu-oxidase
(74)
Melanocarpus albomyces
(2)
1a
Cu-oxidase-2q9oB01
B:166-315
1b
Cu-oxidase-2q9oB02
B:166-315
Family
:
Cu-oxidase_2
(24)
Melanocarpus albomyces
(2)
2a
Cu-oxidase_2-2q9oB03
B:359-523
2b
Cu-oxidase_2-2q9oB04
B:359-523
Family
:
Cu-oxidase_3
(79)
Melanocarpus albomyces
(2)
3a
Cu-oxidase_3-2q9oB05
B:41-160
3b
Cu-oxidase_3-2q9oB06
B:41-160
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
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Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
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Chain C
Chain D
Chain E
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Asymmetric Unit 1
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Miscellaneous
Script
Example Commands
Example Command
Action
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)
[
close Script example commands
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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