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3HDL
Asym. Unit
Info
Asym.Unit (132 KB)
Biol.Unit 1 (120 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HIGHLY GLYCOSYLATED PEROXIDASE FROM ROYAL PALM TREE
Authors
:
L. Watanabe, P. R. Moura, L. Bleicher, A. S. Nascimento, L. S. Zamorano, J. J. Calvete, S. Bursakov, M. G. Roig, V. L. Shnyrov, I. Polikarpov
Date
:
07 May 09 (Deposition) - 24 Nov 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Peroxidase, Palm Tree, Glycosylated, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Watanabe, P. R. De Moura, L. Bleicher, A. S. Nascimento, L. S. Zamorano, J. J. Calvete, L. Sanz, A. Perez, S. Bursakov, M. G. Roig V. L. Shnyrov, I. Polikarpov
Crystal Structure And Statistical Coupling Analysis Of Highly Glycosylated Peroxidase From Royal Palm Tree (Roystonea Regia).
J. Struct. Biol. V. 169 226 2010
[
close entry info
]
Hetero Components
(10, 58)
Info
All Hetero Components
01a: CALCIUM ION (CAa)
01b: CALCIUM ION (CAb)
02a: 1,2-ETHANEDIOL (EDOa)
02b: 1,2-ETHANEDIOL (EDOb)
02c: 1,2-ETHANEDIOL (EDOc)
02d: 1,2-ETHANEDIOL (EDOd)
02e: 1,2-ETHANEDIOL (EDOe)
02f: 1,2-ETHANEDIOL (EDOf)
02g: 1,2-ETHANEDIOL (EDOg)
02h: 1,2-ETHANEDIOL (EDOh)
02i: 1,2-ETHANEDIOL (EDOi)
02j: 1,2-ETHANEDIOL (EDOj)
02k: 1,2-ETHANEDIOL (EDOk)
02l: 1,2-ETHANEDIOL (EDOl)
02m: 1,2-ETHANEDIOL (EDOm)
02n: 1,2-ETHANEDIOL (EDOn)
02o: 1,2-ETHANEDIOL (EDOo)
02p: 1,2-ETHANEDIOL (EDOp)
03a: ALPHA-L-FUCOSE (FUCa)
03b: ALPHA-L-FUCOSE (FUCb)
03c: ALPHA-L-FUCOSE (FUCc)
03d: ALPHA-L-FUCOSE (FUCd)
03e: ALPHA-L-FUCOSE (FUCe)
04a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
05a: ALPHA-D-MANNOSE (MANa)
05b: ALPHA-D-MANNOSE (MANb)
05c: ALPHA-D-MANNOSE (MANc)
05d: ALPHA-D-MANNOSE (MANd)
05e: ALPHA-D-MANNOSE (MANe)
05f: ALPHA-D-MANNOSE (MANf)
05g: ALPHA-D-MANNOSE (MANg)
05h: ALPHA-D-MANNOSE (MANh)
06a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
07a: N-ACETYL-D-GLUCOSAMINE (NAGa)
07b: N-ACETYL-D-GLUCOSAMINE (NAGb)
07c: N-ACETYL-D-GLUCOSAMINE (NAGc)
07d: N-ACETYL-D-GLUCOSAMINE (NAGd)
07e: N-ACETYL-D-GLUCOSAMINE (NAGe)
07f: N-ACETYL-D-GLUCOSAMINE (NAGf)
07g: N-ACETYL-D-GLUCOSAMINE (NAGg)
07h: N-ACETYL-D-GLUCOSAMINE (NAGh)
07i: N-ACETYL-D-GLUCOSAMINE (NAGi)
07j: N-ACETYL-D-GLUCOSAMINE (NAGj)
07k: N-ACETYL-D-GLUCOSAMINE (NAGk)
07l: N-ACETYL-D-GLUCOSAMINE (NAGl)
07m: N-ACETYL-D-GLUCOSAMINE (NAGm)
07n: N-ACETYL-D-GLUCOSAMINE (NAGn)
07o: N-ACETYL-D-GLUCOSAMINE (NAGo)
08a: HYDROGEN PEROXIDE (PEOa)
09a: SULFATE ION (SO4a)
09b: SULFATE ION (SO4b)
09c: SULFATE ION (SO4c)
09d: SULFATE ION (SO4d)
09e: SULFATE ION (SO4e)
09f: SULFATE ION (SO4f)
09g: SULFATE ION (SO4g)
09h: SULFATE ION (SO4h)
10a: BETA-D-XYLOFURANOSE (XYZa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
EDO
16
Ligand/Ion
1,2-ETHANEDIOL
3
FUC
5
Ligand/Ion
ALPHA-L-FUCOSE
4
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
5
MAN
8
Ligand/Ion
ALPHA-D-MANNOSE
6
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
7
NAG
15
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
PEO
1
Ligand/Ion
HYDROGEN PEROXIDE
9
SO4
8
Ligand/Ion
SULFATE ION
10
XYZ
1
Ligand/Ion
BETA-D-XYLOFURANOSE
[
close Hetero Component info
]
Sites
(58, 58)
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)
55: GC1 (SOFTWARE)
56: GC2 (SOFTWARE)
57: GC3 (SOFTWARE)
58: GC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:34 , ARG A:38 , PHE A:41 , SER A:73 , ARG A:75 , SER A:140 , PRO A:141 , LEU A:148 , PHE A:152 , LEU A:165 , SER A:166 , ALA A:168 , HIS A:169 , GLY A:172 , VAL A:173 , ALA A:174 , HIS A:175 , SER A:178 , LEU A:222 , LEU A:245 , SER A:247 , PEO A:309 , HOH A:592 , HOH A:593 , HOH A:714
BINDING SITE FOR RESIDUE HEM A 305
02
AC2
SOFTWARE
SER A:170 , ASP A:223 , THR A:226 , VAL A:229 , ASP A:231
BINDING SITE FOR RESIDUE CA A 306
03
AC3
SOFTWARE
ASP A:43 , VAL A:46 , GLY A:48 , ASP A:50 , SER A:52 , HOH A:594
BINDING SITE FOR RESIDUE CA A 307
04
AC4
SOFTWARE
ARG A:38 , PHE A:41 , HIS A:42 , HEM A:305 , HOH A:376 , HOH A:587
BINDING SITE FOR RESIDUE PEO A 309
05
AC5
SOFTWARE
SO4 A:312 , HOH A:435 , HOH A:436 , NAG A:500 , NAG A:501 , MAN A:504 , HOH A:607 , HOH A:837
BINDING SITE FOR RESIDUE SO4 A 311
06
AC6
SOFTWARE
ARG A:75 , GLY A:76 , PHE A:77 , GLU A:78 , SO4 A:311 , EDO A:332 , MAN A:504 , HOH A:665 , HOH A:695
BINDING SITE FOR RESIDUE SO4 A 312
07
AC7
SOFTWARE
NAG A:400 , NAG A:401 , MAN A:404 , HOH A:421
BINDING SITE FOR RESIDUE SO4 A 313
08
AC8
SOFTWARE
PRO A:198 , ILE A:225 , THR A:226 , PRO A:227 , SER A:228 , VAL A:229 , HOH A:310 , HOH A:625
BINDING SITE FOR RESIDUE SO4 A 314
09
AC9
SOFTWARE
TYR A:117 , GLN A:118 , HOH A:445 , HOH A:735
BINDING SITE FOR RESIDUE SO4 A 315
10
BC1
SOFTWARE
SER A:273 , HOH A:473 , HOH A:736 , NAG A:900 , NAG A:901
BINDING SITE FOR RESIDUE SO4 A 316
11
BC2
SOFTWARE
NAG A:800 , NAG A:801 , HOH A:848 , HOH A:925
BINDING SITE FOR RESIDUE SO4 A 317
12
BC3
SOFTWARE
GLN A:93 , NAG A:600 , NAG A:601 , HOH A:811
BINDING SITE FOR RESIDUE SO4 A 318
13
BC4
SOFTWARE
THR A:13 , PRO A:141 , SER A:177 , THR A:213 , ARG A:214 , EDO A:329 , HOH A:590 , HOH A:591
BINDING SITE FOR RESIDUE MES A 319
14
BC5
SOFTWARE
SER A:199 , LEU A:203 , VAL A:220 , SER A:221 , HOH A:368 , HOH A:516
BINDING SITE FOR RESIDUE EDO A 320
15
BC6
SOFTWARE
GLN A:277 , VAL A:280 , LYS A:281 , GLN A:284 , HOH A:483 , HOH A:692 , HOH A:713 , HOH A:864
BINDING SITE FOR RESIDUE EDO A 321
16
BC7
SOFTWARE
ASN A:232 , ALA A:265 , MET A:266 , ASN A:267 , LEU A:268
BINDING SITE FOR RESIDUE EDO A 322
17
BC8
SOFTWARE
ARG A:205 , HOH A:746
BINDING SITE FOR RESIDUE EDO A 323
18
BC9
SOFTWARE
THR A:9 , PRO A:12 , THR A:180 , TYR A:184 , ASN A:185 , HOH A:467 , HOH A:488 , HOH A:744
BINDING SITE FOR RESIDUE EDO A 324
19
CC1
SOFTWARE
ARG A:47 , HOH A:828
BINDING SITE FOR RESIDUE EDO A 326
20
CC2
SOFTWARE
ASN A:114 , LEU A:268 , ALA A:272 , EDO A:334 , HOH A:549 , HOH A:911
BINDING SITE FOR RESIDUE EDO A 327
21
CC3
SOFTWARE
THR A:62 , ASP A:66 , ASN A:135 , HOH A:441 , HOH A:835
BINDING SITE FOR RESIDUE EDO A 328
22
CC4
SOFTWARE
SER A:16 , LEU A:17 , GLN A:20 , ARG A:214 , PHE A:215 , MES A:319 , HOH A:937
BINDING SITE FOR RESIDUE EDO A 329
23
CC5
SOFTWARE
TYR A:184 , ASN A:185 , ARG A:205 , HOH A:496
BINDING SITE FOR RESIDUE EDO A 330
24
CC6
SOFTWARE
ASN A:70 , ASN A:71 , PRO A:72 , LEU A:74 , PHE A:77 , HOH A:363 , MAN A:504 , HOH A:709 , HOH A:896
BINDING SITE FOR RESIDUE EDO A 331
25
CC7
SOFTWARE
LYS A:65 , PHE A:77 , SO4 A:312 , MAN A:504 , HOH A:627 , HOH A:708 , HOH A:737
BINDING SITE FOR RESIDUE EDO A 332
26
CC8
SOFTWARE
GLY A:5 , TYR A:7 , CYS A:11 , PRO A:12 , GLU A:15
BINDING SITE FOR RESIDUE EDO A 333
27
CC9
SOFTWARE
ILE A:115 , THR A:116 , ALA A:272 , SER A:273 , EDO A:327 , HOH A:339
BINDING SITE FOR RESIDUE EDO A 334
28
DC1
SOFTWARE
ARG A:75 , ILE A:171 , GLY A:172 , PRO A:227 , SER A:228 , HOH A:661 , HOH A:923
BINDING SITE FOR RESIDUE EDO A 335
29
DC2
SOFTWARE
THR A:158 , ASP A:160 , HOH A:754 , HOH A:795 , HOH A:898
BINDING SITE FOR RESIDUE EDO A 336
30
DC3
SOFTWARE
ILE A:4 , GLY A:5 , ASN A:8 , SO4 A:313 , NAG A:401 , FUC A:402 , HOH A:677 , HOH A:774 , HOH A:910
BINDING SITE FOR RESIDUE NAG A 400
31
DC4
SOFTWARE
GLN A:118 , SO4 A:313 , HOH A:360 , NAG A:400 , FUC A:402 , MAN A:403 , MAN A:404 , HOH A:677 , HOH A:774 , HOH A:867
BINDING SITE FOR RESIDUE NAG A 401
32
DC5
SOFTWARE
ILE A:4 , HOH A:359 , NAG A:400 , NAG A:401 , HOH A:439 , HOH A:774 , HOH A:875
BINDING SITE FOR RESIDUE FUC A 402
33
DC6
SOFTWARE
NAG A:401 , MAN A:404 , MAN A:405 , XYZ A:406 , HOH A:520
BINDING SITE FOR RESIDUE MAN A 403
34
DC7
SOFTWARE
SO4 A:313 , NAG A:401 , MAN A:403 , HOH A:478
BINDING SITE FOR RESIDUE MAN A 404
35
DC8
SOFTWARE
MAN A:403 , HOH A:520
BINDING SITE FOR RESIDUE MAN A 405
36
DC9
SOFTWARE
MAN A:403 , HOH A:570
BINDING SITE FOR RESIDUE XYZ A 406
37
EC1
SOFTWARE
ASN A:28 , ALA A:59 , SO4 A:311 , HOH A:347 , HOH A:379 , NAG A:501 , FUC A:502 , HOH A:734
BINDING SITE FOR RESIDUE NAG A 500
38
EC2
SOFTWARE
SO4 A:311 , HOH A:349 , NAG A:500 , FUC A:502 , MAN A:503 , MAN A:504
BINDING SITE FOR RESIDUE NAG A 501
39
EC3
SOFTWARE
ASN A:60 , NAG A:500 , NAG A:501
BINDING SITE FOR RESIDUE FUC A 502
40
EC4
SOFTWARE
HOH A:349 , NAG A:501 , MAN A:504 , HOH A:935
BINDING SITE FOR RESIDUE MAN A 503
41
EC5
SOFTWARE
PHE A:77 , SO4 A:311 , SO4 A:312 , EDO A:331 , EDO A:332 , HOH A:349 , HOH A:436 , HOH A:451 , HOH A:491 , NAG A:501 , MAN A:503 , HOH A:561 , HOH A:665 , HOH A:709
BINDING SITE FOR RESIDUE MAN A 504
42
EC6
SOFTWARE
ASN A:144 , GLN A:147 , SO4 A:318 , HOH A:493 , NAG A:601 , FUC A:602 , HOH A:811
BINDING SITE FOR RESIDUE NAG A 600
43
EC7
SOFTWARE
SO4 A:318 , HOH A:477 , NAG A:600 , FUC A:602
BINDING SITE FOR RESIDUE NAG A 601
44
EC8
SOFTWARE
HOH A:341 , HOH A:581 , NAG A:600 , NAG A:601
BINDING SITE FOR RESIDUE FUC A 602
45
EC9
SOFTWARE
ASN A:154 , HOH A:308
BINDING SITE FOR RESIDUE NAG A 700
46
FC1
SOFTWARE
ASN A:211 , SO4 A:317 , HOH A:389 , HOH A:697 , NAG A:801 , FUC A:802
BINDING SITE FOR RESIDUE NAG A 800
47
FC2
SOFTWARE
SO4 A:317 , NAG A:800 , FUC A:802
BINDING SITE FOR RESIDUE NAG A 801
48
FC3
SOFTWARE
NAG A:800 , NAG A:801
BINDING SITE FOR RESIDUE FUC A 802
49
FC4
SOFTWARE
ASN A:267 , THR A:269 , ALA A:270 , SO4 A:316 , HOH A:408 , HOH A:460 , HOH A:533 , NAG A:901
BINDING SITE FOR RESIDUE NAG A 900
50
FC5
SOFTWARE
SO4 A:316 , NAG A:900
BINDING SITE FOR RESIDUE NAG A 901
51
FC6
SOFTWARE
ASP A:56 , ASN A:298 , SER A:300 , VAL A:301 , HOH A:380 , HOH A:722 , HOH A:752 , HOH A:902 , NAG A:1001 , FUC A:1002
BINDING SITE FOR RESIDUE NAG A 1000
52
FC7
SOFTWARE
ASP A:56 , HOH A:380 , HOH A:562 , NAG A:1000 , FUC A:1002 , MAN A:1003 , MAN A:1004
BINDING SITE FOR RESIDUE NAG A 1001
53
FC8
SOFTWARE
HOH A:380 , HOH A:396 , NAG A:1000 , NAG A:1001
BINDING SITE FOR RESIDUE FUC A 1002
54
FC9
SOFTWARE
HOH A:527 , NAG A:1001 , MAN A:1004 , MAN A:1005
BINDING SITE FOR RESIDUE MAN A 1003
55
GC1
SOFTWARE
HOH A:348 , HOH A:391 , NAG A:1001 , MAN A:1003 , MAN A:1005
BINDING SITE FOR RESIDUE MAN A 1004
56
GC2
SOFTWARE
MAN A:1003 , MAN A:1004
BINDING SITE FOR RESIDUE MAN A 1005
57
GC3
SOFTWARE
ASN A:114 , HOH A:497 , HOH A:508 , HOH A:532 , HOH A:554
BINDING SITE FOR RESIDUE NAG A 1100
58
GC4
SOFTWARE
ASN A:256 , HOH A:495
BINDING SITE FOR RESIDUE NAG A 1200
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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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
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
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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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3hdla_ (A:)
View:
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Classes
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Folds
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Superfamilies
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Heme-dependent peroxidases
(402)
Superfamily
:
Heme-dependent peroxidases
(402)
Family
:
automated matches
(40)
Protein domain
:
automated matches
(40)
Roystonea regia [TaxId: 145709]
(1)
1a
d3hdla_
A:
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_3hdlA01 (A:1-138,A:283-304)
2a: CATH_3hdlA02 (A:139-282)
View:
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Peroxidase; domain 1
(244)
Homologous Superfamily
:
[code=1.10.520.10, no name defined]
(241)
Roystonea regia. Organism_taxid: 145709
(1)
1a
3hdlA01
A:1-138,A:283-304
Topology
:
Peroxidase; domain 2
(241)
Homologous Superfamily
:
Peroxidase, domain 2
(241)
Roystonea regia. Organism_taxid: 145709
(1)
2a
3hdlA02
A:139-282
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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select residue range 5 to 10 in chain 'A'
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