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2PCD
Biol. Unit 8
Info
Asym.Unit (446 KB)
Biol.Unit 1 (80 KB)
Biol.Unit 10 (152 KB)
Biol.Unit 11 (152 KB)
Biol.Unit 2 (80 KB)
Biol.Unit 3 (80 KB)
Biol.Unit 4 (80 KB)
Biol.Unit 5 (80 KB)
Biol.Unit 6 (80 KB)
Biol.Unit 7 (867 KB)
Biol.Unit 8 (151 KB)
Biol.Unit 9 (152 KB)
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(1)
Title
:
STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE FROM PSEUDOMONAS AERUGINOSA AT 2.15 ANGSTROMS RESOLUTION
Authors
:
D. H. Ohlendorf, A. M. Orville, J. D. Lipscomb
Date
:
21 Jun 94 (Deposition) - 20 Dec 94 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D,E,F,M,N,O,P,Q,R
Biol. Unit 1: A,M (1x)
Biol. Unit 2: B,N (1x)
Biol. Unit 3: C,O (1x)
Biol. Unit 4: D,P (1x)
Biol. Unit 5: E,Q (1x)
Biol. Unit 6: F,R (1x)
Biol. Unit 7: A,B,C,D,E,F,M,N,O,P,Q,R (2x)
Biol. Unit 8: E,Q (2x)
Biol. Unit 9: A,D,M,P (1x)
Biol. Unit 10: B,N (2x)
Biol. Unit 11: C,F,O,R (1x)
Keywords
:
Dioxygenase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
D. H. Ohlendorf, A. M. Orville, J. D. Lipscomb
Structure Of Protocatechuate 3, 4-Dioxygenase From Pseudomonas Aeruginosa At 2. 15 A Resolution.
J. Mol. Biol. V. 244 586 1994
(for further references see the
PDB file header
)
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Hetero Components
(0, 0)
Info
All Hetero Components
1a: FE (III) ION (FEa)
1b: FE (III) ION (FEb)
1c: FE (III) ION (FEc)
1d: FE (III) ION (FEd)
1e: FE (III) ION (FEe)
1f: FE (III) ION (FEf)
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Sites
(5, 5)
Info
All Sites
1: AC5 (SOFTWARE)
2: ACE (AUTHOR)
3: ACF (AUTHOR)
4: VEE (AUTHOR)
5: VEF (AUTHOR)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
TYR Q:408 , TYR Q:447 , HIS Q:460 , HIS Q:462 , HOH Q:1183
BINDING SITE FOR RESIDUE FE Q 600
2
ACE
AUTHOR
THR E:12 , ALA E:13 , GLY E:14 , PRO E:15 , TYR E:16 , ARG E:133 , GLY E:134 , TYR Q:324 , THR Q:326 , TYR Q:408 , TYR Q:447 , TRP Q:449 , ARG Q:450 , ARG Q:457 , HIS Q:460 , HIS Q:462 , GLN Q:477 , ILE Q:491 , FE Q:600 , HOH E:208 , HOH Q:999 , HOH Q:1015 , HOH Q:1016 , HOH Q:1034 , HOH Q:1092 , HOH Q:1119 , HOH Q:1155 , HOH Q:1157 , HOH Q:1183
active site
3
ACF
AUTHOR
THR F:12 , ALA F:13 , GLY F:14 , PRO F:15 , TYR F:16 , ARG F:133 , GLY F:134 , TYR R:324 , THR R:326 , TYR R:408 , TYR R:447 , TRP R:449 , ARG R:450 , ARG R:457 , HIS R:460 , HIS R:462 , GLN R:477 , ILE R:491 , FE R:600 , HOH E:208 , HOH Q:999 , HOH Q:1015 , HOH Q:1016 , HOH Q:1034 , HOH Q:1092 , HOH Q:1119 , HOH Q:1155 , HOH Q:1157 , HOH Q:1183
active site
4
VEE
AUTHOR
TYR E:79 , VAL E:114 , ASN E:115 , ASN E:116 , ALA E:117 , ALA E:118 , MET E:122 , HIS E:125 , ASN E:127 , ARG E:142 , VAL E:157 , ASP Q:304 , ARG Q:307 , ILE Q:339 , PRO Q:340 , GLN Q:341 , SER Q:342 , ILE Q:343 , SER Q:344 , GLU Q:345 , HOH E:223 , HOH Q:1011 , HOH Q:1022 , HOH E:233 , HOH Q:1037 , HOH E:236 , HOH Q:1063 , HOH E:246 , HOH Q:1151
vestigial site
5
VEF
AUTHOR
TYR F:79 , VAL F:114 , ASN F:115 , ASN F:116 , ALA F:117 , ALA F:118 , MET F:122 , HIS F:125 , ASN F:127 , ARG F:142 , VAL F:157 , ASP R:304 , ARG R:307 , ILE R:339 , PRO R:340 , GLN R:341 , SER R:342 , ILE R:343 , SER R:344 , GLU R:345 , HOH E:223 , HOH Q:1011 , HOH Q:1022 , HOH E:233 , HOH Q:1037 , HOH E:236 , HOH Q:1063 , HOH E:246 , HOH Q:1151
vestigial site
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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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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: INTRADIOL_DIOXYGENAS (Q:380-408)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INTRADIOL_DIOXYGENAS
PS00083
Intradiol ring-cleavage dioxygenases signature.
PCXA_PSEPU
52-80
2
-
-
-
-
E:51-79
-
PCXB_PSEPU
81-109
2
-
-
-
-
Q:380-408
-
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Exons
(0, 0)
Info
All Exons
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d2pcda_ (A:)
1b: SCOP_d2pcdb_ (B:)
1c: SCOP_d2pcdc_ (C:)
1d: SCOP_d2pcdd_ (D:)
1e: SCOP_d2pcde_ (E:)
1f: SCOP_d2pcdf_ (F:)
2a: SCOP_d2pcdm_ (M:)
2b: SCOP_d2pcdn_ (N:)
2c: SCOP_d2pcdo_ (O:)
2d: SCOP_d2pcdp_ (P:)
2e: SCOP_d2pcdq_ (Q:)
2f: SCOP_d2pcdr_ (R:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
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(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Prealbumin-like
(433)
Superfamily
:
Aromatic compound dioxygenase
(111)
Family
:
Aromatic compound dioxygenase
(100)
Protein domain
:
Protocatechuate-3,4-dioxygenase, alpha chain
(37)
Pseudomonas putida [TaxId: 303]
(31)
1a
d2pcda_
A:
1b
d2pcdb_
B:
1c
d2pcdc_
C:
1d
d2pcdd_
D:
1e
d2pcde_
E:
1f
d2pcdf_
F:
Protein domain
:
Protocatechuate-3,4-dioxygenase, beta chain
(44)
Pseudomonas putida [TaxId: 303]
(31)
2a
d2pcdm_
M:
2b
d2pcdn_
N:
2c
d2pcdo_
O:
2d
d2pcdp_
P:
2e
d2pcdq_
Q:
2f
d2pcdr_
R:
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CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_2pcdM00 (M:301-536)
1b: CATH_2pcdN00 (N:301-536)
1c: CATH_2pcdE00 (E:1-200)
1d: CATH_2pcdF00 (F:1-200)
1e: CATH_2pcdO00 (O:301-536)
1f: CATH_2pcdP00 (P:301-536)
1g: CATH_2pcdQ00 (Q:301-536)
1h: CATH_2pcdR00 (R:301-536)
1i: CATH_2pcdA00 (A:1-200)
1j: CATH_2pcdB00 (B:1-200)
1k: CATH_2pcdC00 (C:1-200)
1l: CATH_2pcdD00 (D:1-200)
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Architectures
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Topologies
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)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Protocatechuate 3,4-Dioxygenase, subunit A
(43)
Homologous Superfamily
:
Protocatechuate 3,4-Dioxygenase, subunit A
(43)
Pseudomonas putida. Organism_taxid: 303.
(1)
1a
2pcdM00
M:301-536
1b
2pcdN00
N:301-536
1c
2pcdE00
E:1-200
1d
2pcdF00
F:1-200
1e
2pcdO00
O:301-536
1f
2pcdP00
P:301-536
1g
2pcdQ00
Q:301-536
1h
2pcdR00
R:301-536
1i
2pcdA00
A:1-200
1j
2pcdB00
B:1-200
1k
2pcdC00
C:1-200
1l
2pcdD00
D:1-200
[
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Pfam Domains
(2, 18)
Info
all PFAM domains
1a: PFAM_Dioxygenase_C_2pcdF01 (F:23-192)
1b: PFAM_Dioxygenase_C_2pcdF02 (F:23-192)
1c: PFAM_Dioxygenase_C_2pcdF03 (F:23-192)
1d: PFAM_Dioxygenase_C_2pcdF04 (F:23-192)
1e: PFAM_Dioxygenase_C_2pcdF05 (F:23-192)
1f: PFAM_Dioxygenase_C_2pcdF06 (F:23-192)
1g: PFAM_Dioxygenase_C_2pcdR01 (R:346-530)
1h: PFAM_Dioxygenase_C_2pcdR02 (R:346-530)
1i: PFAM_Dioxygenase_C_2pcdR03 (R:346-530)
1j: PFAM_Dioxygenase_C_2pcdR04 (R:346-530)
1k: PFAM_Dioxygenase_C_2pcdR05 (R:346-530)
1l: PFAM_Dioxygenase_C_2pcdR06 (R:346-530)
2a: PFAM_PCDO_beta_N_2pcdR07 (R:308-343)
2b: PFAM_PCDO_beta_N_2pcdR08 (R:308-343)
2c: PFAM_PCDO_beta_N_2pcdR09 (R:308-343)
2d: PFAM_PCDO_beta_N_2pcdR10 (R:308-343)
2e: PFAM_PCDO_beta_N_2pcdR11 (R:308-343)
2f: PFAM_PCDO_beta_N_2pcdR12 (R:308-343)
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Clans
(
)
(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Transthyretin
(88)
Family
:
Dioxygenase_C
(32)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(27)
1a
Dioxygenase_C-2pcdF01
F:23-192
1b
Dioxygenase_C-2pcdF02
F:23-192
1c
Dioxygenase_C-2pcdF03
F:23-192
1d
Dioxygenase_C-2pcdF04
F:23-192
1e
Dioxygenase_C-2pcdF05
F:23-192
1f
Dioxygenase_C-2pcdF06
F:23-192
1g
Dioxygenase_C-2pcdR01
R:346-530
1h
Dioxygenase_C-2pcdR02
R:346-530
1i
Dioxygenase_C-2pcdR03
R:346-530
1j
Dioxygenase_C-2pcdR04
R:346-530
1k
Dioxygenase_C-2pcdR05
R:346-530
1l
Dioxygenase_C-2pcdR06
R:346-530
Clan
:
no clan defined [family: PCDO_beta_N]
(26)
Family
:
PCDO_beta_N
(26)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(26)
2a
PCDO_beta_N-2pcdR07
R:308-343
2b
PCDO_beta_N-2pcdR08
R:308-343
2c
PCDO_beta_N-2pcdR09
R:308-343
2d
PCDO_beta_N-2pcdR10
R:308-343
2e
PCDO_beta_N-2pcdR11
R:308-343
2f
PCDO_beta_N-2pcdR12
R:308-343
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