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4A5G
Biol. Unit 1
Info
Asym.Unit (136 KB)
Biol.Unit 1 (65 KB)
Biol.Unit 2 (63 KB)
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(1)
Title
:
RAPHANUS SATIVUS ANIONIC PEROXIDASE.
Authors
:
N. Jimenez-Arroyo, B. Valderrama, P. Gil-Rodriguez, S. P. Rojas-Trej E. Rudino-Pinera
Date
:
25 Oct 11 (Deposition) - 07 Nov 12 (Release) - 16 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Oxidoreductase, Glycoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Gil-Rodriguez, N. Jimenez-Arroyo, S. P. Rojas-Trejo, E. Rudino-Pinera, B. Valderrama
Crystallographic Structure Of The Raphanus Sativus Anionic Peroxidase
To Be Published
[
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Hetero Components
(8, 30)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
1c: PENTAETHYLENE GLYCOL (1PEc)
1d: PENTAETHYLENE GLYCOL (1PEd)
1e: PENTAETHYLENE GLYCOL (1PEe)
1f: PENTAETHYLENE GLYCOL (1PEf)
1g: PENTAETHYLENE GLYCOL (1PEg)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
2c: BETA-D-MANNOSE (BMAc)
2d: BETA-D-MANNOSE (BMAd)
2e: BETA-D-MANNOSE (BMAe)
2f: BETA-D-MANNOSE (BMAf)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
3d: CALCIUM ION (CAd)
4a: ALPHA-L-FUCOSE (FUCa)
4b: ALPHA-L-FUCOSE (FUCb)
4c: ALPHA-L-FUCOSE (FUCc)
4d: ALPHA-L-FUCOSE (FUCd)
4e: ALPHA-L-FUCOSE (FUCe)
4f: ALPHA-L-FUCOSE (FUCf)
5a: BETA-L-FUCOSE (FULa)
5b: BETA-L-FUCOSE (FULb)
5c: BETA-L-FUCOSE (FULc)
6a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
6b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
7a: ALPHA-D-MANNOSE (MANa)
7b: ALPHA-D-MANNOSE (MANb)
7c: ALPHA-D-MANNOSE (MANc)
7d: ALPHA-D-MANNOSE (MANd)
7e: ALPHA-D-MANNOSE (MANe)
8a: N-ACETYL-D-GLUCOSAMINE (NAGa)
8b: N-ACETYL-D-GLUCOSAMINE (NAGb)
8c: N-ACETYL-D-GLUCOSAMINE (NAGc)
8d: N-ACETYL-D-GLUCOSAMINE (NAGd)
8e: N-ACETYL-D-GLUCOSAMINE (NAGe)
8f: N-ACETYL-D-GLUCOSAMINE (NAGf)
8g: N-ACETYL-D-GLUCOSAMINE (NAGg)
8h: N-ACETYL-D-GLUCOSAMINE (NAGh)
8i: N-ACETYL-D-GLUCOSAMINE (NAGi)
8j: N-ACETYL-D-GLUCOSAMINE (NAGj)
8k: N-ACETYL-D-GLUCOSAMINE (NAGk)
8l: N-ACETYL-D-GLUCOSAMINE (NAGl)
8m: N-ACETYL-D-GLUCOSAMINE (NAGm)
8n: N-ACETYL-D-GLUCOSAMINE (NAGn)
8o: N-ACETYL-D-GLUCOSAMINE (NAGo)
8p: N-ACETYL-D-GLUCOSAMINE (NAGp)
8q: N-ACETYL-D-GLUCOSAMINE (NAGq)
8r: N-ACETYL-D-GLUCOSAMINE (NAGr)
8s: N-ACETYL-D-GLUCOSAMINE (NAGs)
8t: N-ACETYL-D-GLUCOSAMINE (NAGt)
8u: N-ACETYL-D-GLUCOSAMINE (NAGu)
8v: N-ACETYL-D-GLUCOSAMINE (NAGv)
8w: N-ACETYL-D-GLUCOSAMINE (NAGw)
8x: N-ACETYL-D-GLUCOSAMINE (NAGx)
9a: 2-(2-METHOXYETHOXY)ETHANOL (PG0a)
10a: BETA-D-XYLOPYRANOSE (XYPa)
10b: BETA-D-XYLOPYRANOSE (XYPb)
10c: BETA-D-XYLOPYRANOSE (XYPc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
2
Ligand/Ion
PENTAETHYLENE GLYCOL
2
BMA
4
Ligand/Ion
BETA-D-MANNOSE
3
CA
-1
Ligand/Ion
CALCIUM ION
4
FUC
3
Ligand/Ion
ALPHA-L-FUCOSE
5
FUL
2
Ligand/Ion
BETA-L-FUCOSE
6
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
7
MAN
3
Ligand/Ion
ALPHA-D-MANNOSE
8
NAG
13
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
9
PG0
-1
Ligand/Ion
2-(2-METHOXYETHOXY)ETHANOL
10
XYP
2
Ligand/Ion
BETA-D-XYLOPYRANOSE
[
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Sites
(14, 14)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC7 (SOFTWARE)
09: BC8 (SOFTWARE)
10: BC9 (SOFTWARE)
11: CC1 (SOFTWARE)
12: CC2 (SOFTWARE)
13: CC3 (SOFTWARE)
14: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:33 , ALA A:36 , SER A:37 , ARG A:40 , PHE A:43 , SER A:75 , SER A:142 , PRO A:143 , PHE A:154 , LEU A:167 , SER A:168 , ALA A:170 , HIS A:171 , PHE A:173 , GLY A:174 , ARG A:175 , ALA A:176 , THR A:177 , VAL A:180 , LEU A:222 , SER A:247 , HOH A:2057 , HOH A:2058 , HOH A:2329
BINDING SITE FOR RESIDUE HEM A1307
02
AC2
SOFTWARE
ASP A:45 , VAL A:48 , GLY A:50 , ASP A:52 , SER A:54 , HOH A:2062
BINDING SITE FOR RESIDUE CA A1308
03
AC3
SOFTWARE
THR A:172 , ASP A:223 , THR A:226 , ALA A:229 , ASP A:231
BINDING SITE FOR RESIDUE CA A1309
04
AC4
SOFTWARE
GLN A:145 , ASN A:149 , HOH A:2169
BINDING SITE FOR RESIDUE NAG A1336
05
AC5
SOFTWARE
GLY A:2 , SER A:3 , LEU A:4 , ASN A:286
BINDING SITE FOR RESIDUE 1PE A1337
06
AC6
SOFTWARE
PHE A:28 , LEU A:113 , SER A:114 , XYP A:1315 , HOH A:2339 , HOH A:2340 , HOH A:2341
BINDING SITE FOR RESIDUE 1PE A1338
07
BC2
SOFTWARE
ALA A:10 , GLY B:1 , SER B:112 , GLY B:115 , XYP B:1313 , MAN B:1314 , 1PE B:1329 , 1PE B:1334 , HOH B:2150 , HOH B:2317 , HOH B:2328 , HOH B:2329 , HOH B:2330 , HOH B:2331
BINDING SITE FOR RESIDUE 1PE B1330
08
BC7
SOFTWARE
ASN A:5 , PHE A:8 , ARG A:21 , GLN A:25 , LEU A:113 , NAG A:1335 , 1PE A:1338 , HOH A:2005 , HOH A:2015 , HOH A:2038 , HOH A:2330 , HOH A:2331 , HOH A:2332 , HOH A:2333 , HOH A:2334 , HOH A:2335 , HOH A:2336 , HOH A:2337 , HOH A:2338 , HOH A:2339 , HOH A:2340 , HOH A:2341 , HOH A:2342 , ALA B:6 , ARG B:21 , SER B:118 , TRP B:119 , THR B:120 , HOH B:2155
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1310 THROUGH XYP A1315 BOUND TO ASN A 5
09
BC8
SOFTWARE
ASN A:15 , ALA A:18 , THR A:22 , MAN A:1314
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1334 THROUGH NAG A1335 BOUND TO ASN A 15
10
BC9
SOFTWARE
ASN A:68 , ALA A:73 , GLN A:133 , ALA A:134 , ASN A:137
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1316 THROUGH FUC A1319 BOUND TO ASN A 137
11
CC1
SOFTWARE
ASN A:187 , GLY A:190 , HOH A:2357 , HOH A:2358 , HOH A:2359 , HOH A:2360
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1328 THROUGH XYP A1333 BOUND TO ASN A 187
12
CC2
SOFTWARE
SER A:155 , ASN A:199 , SER A:240 , ASN A:242 , HOH A:2265 , HOH A:2343 , HOH A:2344 , HOH A:2345 , HOH A:2346 , HOH A:2347 , HOH A:2348
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1320 THROUGH FUL A1323 BOUND TO ASN A 199
13
CC3
SOFTWARE
ASN A:269 , LEU A:272 , GLN A:275 , HOH A:2287 , HOH A:2349 , HOH A:2350 , HOH A:2352 , HOH A:2353 , HOH A:2354 , THR B:12 , PRO B:94 , HOH B:2136 , HOH B:2137
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1324 THROUGH FUC A1327 BOUND TO ASN A 269
14
CC4
SOFTWARE
ALA A:6 , SER A:17 , ARG A:21 , GLN A:108 , SER A:118 , TRP A:119 , THR A:120 , HOH A:2033 , HOH A:2035 , ASN B:5 , PHE B:8 , ARG B:21 , GLN B:25 , LEU B:113 , NAG B:1323 , 1PE B:1329 , 1PE B:1330 , 1PE B:1334 , HOH B:2005 , HOH B:2011 , HOH B:2030 , HOH B:2038 , HOH B:2307 , HOH B:2308 , HOH B:2312 , HOH B:2313 , HOH B:2314 , HOH B:2315 , HOH B:2316 , HOH B:2317 , HOH B:2318
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B1309 THROUGH MAN B1314 BOUND TO ASN B 5
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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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, 2)
Info
All SCOP Domains
1a: SCOP_d4a5ga_ (A:)
1b: SCOP_d4a5gb_ (B:)
View:
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Classes
(
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Superfamilies
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Heme-dependent peroxidases
(402)
Superfamily
:
Heme-dependent peroxidases
(402)
Family
:
CCP-like
(292)
Protein domain
:
automated matches
(48)
Radish (Raphanus sativus) [TaxId: 3726]
(1)
1a
d4a5ga_
A:
1b
d4a5gb_
B:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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