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3PCB
Asym. Unit
Info
Asym.Unit (450 KB)
Biol.Unit 1 (873 KB)
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(1)
Title
:
STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYBENZOATE
Authors
:
N. Elango, A. M. Orville, J. D. Lipscomb, D. H. Ohlendorf
Date
:
25 Apr 97 (Deposition) - 29 Apr 98 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.19
Chains
:
Asym. Unit : A,B,C,D,E,F,M,N,O,P,Q,R
Biol. Unit 1: A,B,C,D,E,F,M,N,O,P,Q,R (2x)
Keywords
:
Dioxygenase, Iron, Nonheme, Metalloprotein, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. M. Orville, N. Elango, J. D. Lipscomb, D. H. Ohlendorf
Structures Of Competitive Inhibitor Complexes Of Protocatechuate 3, 4-Dioxygenase: Multiple Exogenous Ligand Binding Orientations Within The Active Site.
Biochemistry V. 36 10039 1997
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 24)
Info
All Hetero Components
1a: 3-HYDROXYBENZOIC ACID (3HBa)
1b: 3-HYDROXYBENZOIC ACID (3HBb)
1c: 3-HYDROXYBENZOIC ACID (3HBc)
1d: 3-HYDROXYBENZOIC ACID (3HBd)
1e: 3-HYDROXYBENZOIC ACID (3HBe)
1f: 3-HYDROXYBENZOIC ACID (3HBf)
1g: 3-HYDROXYBENZOIC ACID (3HBg)
1h: 3-HYDROXYBENZOIC ACID (3HBh)
1i: 3-HYDROXYBENZOIC ACID (3HBi)
1j: 3-HYDROXYBENZOIC ACID (3HBj)
1k: 3-HYDROXYBENZOIC ACID (3HBk)
1l: 3-HYDROXYBENZOIC ACID (3HBl)
2a: BETA-MERCAPTOETHANOL (BMEa)
2b: BETA-MERCAPTOETHANOL (BMEb)
2c: BETA-MERCAPTOETHANOL (BMEc)
2d: BETA-MERCAPTOETHANOL (BMEd)
2e: BETA-MERCAPTOETHANOL (BMEe)
2f: BETA-MERCAPTOETHANOL (BMEf)
3a: FE (III) ION (FEa)
3b: FE (III) ION (FEb)
3c: FE (III) ION (FEc)
3d: FE (III) ION (FEd)
3e: FE (III) ION (FEe)
3f: FE (III) ION (FEf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3HB
12
Ligand/Ion
3-HYDROXYBENZOIC ACID
2
BME
6
Ligand/Ion
BETA-MERCAPTOETHANOL
3
FE
6
Ligand/Ion
FE (III) 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: ACA (UNKNOWN)
11: ACB (UNKNOWN)
12: ACC (UNKNOWN)
13: ACD (UNKNOWN)
14: ACE (UNKNOWN)
15: ACF (UNKNOWN)
16: BC1 (SOFTWARE)
17: BC2 (SOFTWARE)
18: BC3 (SOFTWARE)
19: BC4 (SOFTWARE)
20: BC5 (SOFTWARE)
21: BC6 (SOFTWARE)
22: BC7 (SOFTWARE)
23: BC8 (SOFTWARE)
24: BC9 (SOFTWARE)
25: CC1 (SOFTWARE)
26: CC2 (SOFTWARE)
27: CC3 (SOFTWARE)
28: CC4 (SOFTWARE)
29: CC5 (SOFTWARE)
30: CC6 (SOFTWARE)
31: VEA (UNKNOWN)
32: VEB (UNKNOWN)
33: VEC (UNKNOWN)
34: VED (UNKNOWN)
35: VEE (UNKNOWN)
36: VEF (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR M:408 , TYR M:447 , HIS M:460 , HIS M:462 , 3HB M:550
BINDING SITE FOR RESIDUE FE M 600
02
AC2
SOFTWARE
TYR N:408 , TYR N:447 , HIS N:460 , HIS N:462 , 3HB N:550
BINDING SITE FOR RESIDUE FE N 600
03
AC3
SOFTWARE
TYR O:408 , TYR O:447 , HIS O:460 , HIS O:462 , 3HB O:550
BINDING SITE FOR RESIDUE FE O 600
04
AC4
SOFTWARE
TYR P:408 , TYR P:447 , HIS P:460 , HIS P:462 , 3HB P:550
BINDING SITE FOR RESIDUE FE P 600
05
AC5
SOFTWARE
TYR Q:408 , TYR Q:447 , HIS Q:460 , HIS Q:462 , 3HB Q:550
BINDING SITE FOR RESIDUE FE Q 600
06
AC6
SOFTWARE
TYR R:408 , TYR R:447 , HIS R:460 , HIS R:462 , 3HB R:550
BINDING SITE FOR RESIDUE FE R 600
07
AC7
SOFTWARE
HIS M:361 , CYS M:429 , SER M:438 , HOH M:688
BINDING SITE FOR RESIDUE BME M 601
08
AC8
SOFTWARE
PRO A:15 , ARG A:133 , TYR M:324 , TYR M:447 , TRP M:449 , ARG M:457 , HIS M:462 , GLN M:477 , ILE M:491 , FE M:600
BINDING SITE FOR RESIDUE 3HB M 550
09
AC9
SOFTWARE
ARG M:333 , HOH M:676
BINDING SITE FOR RESIDUE 3HB M 551
10
ACA
UNKNOWN
THR A:12 , ALA A:13 , GLY A:14 , PRO A:15 , TYR A:16 , ARG A:133 , GLY A:134 , TYR M:324 , THR M:326 , TYR M:408 , TYR M:447 , TRP M:449 , ARG M:450 , ARG M:457 , HIS M:460 , HIS M:462 , GLN M:477 , ILE M:491 , FE M:600 , HOH A:203 , HOH M:624 , HOH M:631 , HOH M:632 , 3HB M:550 , HOH M:738
SITE "ACA" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS A AND M.
11
ACB
UNKNOWN
THR B:12 , ALA B:13 , GLY B:14 , PRO B:15 , TYR B:16 , ARG B:133 , GLY B:134 , TYR N:324 , THR N:326 , TYR N:408 , TYR N:447 , TRP N:449 , ARG N:450 , ARG N:457 , HIS N:460 , HIS N:462 , GLN N:477 , ILE N:491 , FE N:600 , HOH B:242 , HOH N:630 , HOH N:637 , HOH N:638 , 3HB N:550 , HOH N:756
SITE "ACB" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS B AND N.
12
ACC
UNKNOWN
THR C:12 , ALA C:13 , GLY C:14 , PRO C:15 , TYR C:16 , ARG C:133 , GLY C:134 , TYR O:324 , THR O:326 , TYR O:408 , TYR O:447 , TRP O:449 , ARG O:450 , ARG O:457 , HIS O:460 , HIS O:462 , GLN O:477 , ILE O:491 , FE O:600 , HOH C:207 , HOH O:631 , HOH O:639 , HOH O:640 , 3HB O:550 , HOH O:755
SITE "ACC" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS C AND O.
13
ACD
UNKNOWN
THR D:12 , ALA D:13 , GLY D:14 , PRO D:15 , TYR D:16 , ARG D:133 , GLY D:134 , TYR P:324 , THR P:326 , TYR P:408 , TYR P:447 , TRP P:449 , ARG P:450 , ARG P:457 , HIS P:460 , HIS P:462 , GLN P:477 , ILE P:491 , FE P:600 , HOH D:714 , HOH P:633 , HOH P:641 , HOH P:642 , 3HB P:550 , HOH P:748
SITE "ACD" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS D AND P.
14
ACE
UNKNOWN
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:207 , HOH Q:987 , HOH Q:1002 , HOH Q:1003 , 3HB Q:550 , HOH Q:1177
SITE "ACE" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS E AND Q.
15
ACF
UNKNOWN
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 F:1186 , HOH R:1223 , HOH R:1238 , HOH R:1239 , 3HB R:550 , HOH R:1413
SITE "ACF" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS F AND R.
16
BC1
SOFTWARE
HIS N:361 , CYS N:429 , LEU N:430 , SER N:438
BINDING SITE FOR RESIDUE BME N 601
17
BC2
SOFTWARE
PRO B:15 , ARG B:133 , TYR N:324 , TYR N:447 , TRP N:449 , ARG N:457 , HIS N:462 , GLN N:477 , ILE N:491 , FE N:600
BINDING SITE FOR RESIDUE 3HB N 550
18
BC3
SOFTWARE
ARG N:333 , HOH N:687
BINDING SITE FOR RESIDUE 3HB N 551
19
BC4
SOFTWARE
HIS O:361 , CYS O:429 , SER O:438 , HOH O:699
BINDING SITE FOR RESIDUE BME O 601
20
BC5
SOFTWARE
GLY C:14 , PRO C:15 , ARG C:133 , TYR O:324 , TYR O:447 , TRP O:449 , ARG O:457 , HIS O:462 , GLN O:477 , ILE O:491 , FE O:600
BINDING SITE FOR RESIDUE 3HB O 550
21
BC6
SOFTWARE
ARG O:333 , HOH O:688
BINDING SITE FOR RESIDUE 3HB O 551
22
BC7
SOFTWARE
HIS P:361 , CYS P:429 , LEU P:430 , SER P:438 , HOH P:698
BINDING SITE FOR RESIDUE BME P 601
23
BC8
SOFTWARE
GLY D:14 , PRO D:15 , ARG D:133 , TYR P:324 , TYR P:447 , TRP P:449 , ARG P:457 , HIS P:462 , GLN P:477 , ILE P:491 , FE P:600
BINDING SITE FOR RESIDUE 3HB P 550
24
BC9
SOFTWARE
ARG P:333 , HOH P:687 , PRO R:322
BINDING SITE FOR RESIDUE 3HB P 551
25
CC1
SOFTWARE
HIS Q:361 , CYS Q:429 , LEU Q:430 , SER Q:438 , HOH Q:1091
BINDING SITE FOR RESIDUE BME Q 601
26
CC2
SOFTWARE
PRO E:15 , ARG E:133 , TYR Q:324 , TYR Q:447 , TRP Q:449 , ARG Q:457 , HIS Q:462 , GLN Q:477 , ILE Q:491 , FE Q:600
BINDING SITE FOR RESIDUE 3HB Q 550
27
CC3
SOFTWARE
ARG Q:333 , HOH Q:1074
BINDING SITE FOR RESIDUE 3HB Q 551
28
CC4
SOFTWARE
HIS R:361 , CYS R:429 , LEU R:430 , SER R:438 , HOH R:1327
BINDING SITE FOR RESIDUE BME R 601
29
CC5
SOFTWARE
PRO F:15 , ARG F:133 , TYR R:324 , TYR R:447 , TRP R:449 , ARG R:457 , HIS R:462 , GLN R:477 , ILE R:491 , FE R:600
BINDING SITE FOR RESIDUE 3HB R 550
30
CC6
SOFTWARE
ARG R:333 , HOH R:1310
BINDING SITE FOR RESIDUE 3HB R 551
31
VEA
UNKNOWN
TYR A:79 , VAL A:114 , ASN A:115 , ASN A:116 , ALA A:117 , ALA A:118 , MET A:122 , HIS A:125 , ASN A:127 , ARG A:142 , VAL A:157 , ASP M:304 , ARG M:307 , ILE M:339 , PRO M:340 , GLN M:341 , SER M:342 , ILE M:343 , SER M:344 , GLU M:345 , HOH A:219 , HOH A:222 , HOH M:636 , HOH A:231 , HOH M:642 , HOH A:234 , HOH M:657 , HOH A:247 , HOH M:714
SITE "VEA" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS A AND M.
32
VEB
UNKNOWN
TYR B:79 , VAL B:114 , ASN B:115 , ASN B:116 , ALA B:117 , ALA B:118 , MET B:122 , HIS B:125 , ASN B:127 , ARG B:142 , VAL B:157 , ASP N:304 , ARG N:307 , ILE N:339 , PRO N:340 , GLN N:341 , SER N:342 , ILE N:343 , SER N:344 , GLU N:345 , HOH B:282 , HOH B:290 , HOH N:643 , HOH B:308 , HOH N:651 , HOH B:317 , HOH N:666 , HOH B:359 , HOH N:727
SITE "VEB" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS B AND N.
33
VEC
UNKNOWN
TYR C:79 , VAL C:114 , ASN C:115 , ASN C:116 , ALA C:117 , ALA C:118 , MET C:122 , HIS C:125 , ASN C:127 , ARG C:142 , VAL C:157 , ASP O:304 , ARG O:307 , ILE O:339 , PRO O:340 , GLN O:341 , SER O:342 , ILE O:343 , SER O:344 , GLU O:345 , HOH C:220 , HOH C:223 , HOH O:644 , HOH C:231 , HOH O:652 , HOH C:234 , HOH O:668 , HOH C:246 , HOH C:267
SITE "VEC" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS C AND O.
34
VED
UNKNOWN
TYR D:79 , VAL D:114 , ASN D:115 , ASN D:116 , ALA D:117 , ALA D:118 , MET D:122 , HIS D:125 , ASN D:127 , ARG D:142 , VAL D:157 , ASP P:304 , ARG P:307 , ILE P:339 , PRO P:340 , GLN P:341 , SER P:342 , ILE P:343 , SER P:344 , GLU P:345 , HOH D:754 , HOH P:639 , HOH D:773 , HOH D:780 , HOH P:652 , HOH D:789 , HOH P:668 , HOH D:831 , HOH P:723
SITE "VED" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS D AND P.
35
VEE
UNKNOWN
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:222 , HOH Q:998 , HOH E:229 , HOH E:234 , HOH Q:1023 , HOH E:237 , HOH Q:1049 , HOH E:249 , HOH Q:1135
SITE "VEE" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS E AND Q.
36
VEF
UNKNOWN
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 F:1226 , HOH F:1234 , HOH R:1245 , HOH F:1252 , HOH R:1259 , HOH F:1261 , HOH R:1285 , HOH F:1303 , HOH R:1371
SITE "VEF" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS F AND R.
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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[
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PROSITE Patterns/Profiles
(1, 12)
Info
All PROSITE Patterns/Profiles
1: INTRADIOL_DIOXYGENAS (A:51-79,B:51-79,C:51-79,D:51-79,E:...)
;
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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
6
A:51-79
B:51-79
C:51-79
D:51-79
E:51-79
F:51-79
PCXB_PSEPU
81-109
6
M:380-408
N:380-408
O:380-408
P:380-408
Q:380-408
R:380-408
[
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d3pcba_ (A:)
1b: SCOP_d3pcbb_ (B:)
1c: SCOP_d3pcbc_ (C:)
1d: SCOP_d3pcbd_ (D:)
1e: SCOP_d3pcbe_ (E:)
1f: SCOP_d3pcbf_ (F:)
2a: SCOP_d3pcbm_ (M:)
2b: SCOP_d3pcbn_ (N:)
2c: SCOP_d3pcbo_ (O:)
2d: SCOP_d3pcbp_ (P:)
2e: SCOP_d3pcbq_ (Q:)
2f: SCOP_d3pcbr_ (R:)
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Protein Domains
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Organisms
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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
d3pcba_
A:
1b
d3pcbb_
B:
1c
d3pcbc_
C:
1d
d3pcbd_
D:
1e
d3pcbe_
E:
1f
d3pcbf_
F:
Protein domain
:
Protocatechuate-3,4-dioxygenase, beta chain
(44)
Pseudomonas putida [TaxId: 303]
(31)
2a
d3pcbm_
M:
2b
d3pcbn_
N:
2c
d3pcbo_
O:
2d
d3pcbp_
P:
2e
d3pcbq_
Q:
2f
d3pcbr_
R:
[
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CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_3pcbM00 (M:301-536)
1b: CATH_3pcbA00 (A:1-200)
1c: CATH_3pcbB00 (B:1-200)
1d: CATH_3pcbC00 (C:1-200)
1e: CATH_3pcbD00 (D:1-200)
1f: CATH_3pcbE00 (E:1-200)
1g: CATH_3pcbF00 (F:1-200)
1h: CATH_3pcbN00 (N:301-536)
1i: CATH_3pcbO00 (O:301-536)
1j: CATH_3pcbP00 (P:301-536)
1k: CATH_3pcbQ00 (Q:301-536)
1l: CATH_3pcbR00 (R:301-536)
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)
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.
(20)
1a
3pcbM00
M:301-536
1b
3pcbA00
A:1-200
1c
3pcbB00
B:1-200
1d
3pcbC00
C:1-200
1e
3pcbD00
D:1-200
1f
3pcbE00
E:1-200
1g
3pcbF00
F:1-200
1h
3pcbN00
N:301-536
1i
3pcbO00
O:301-536
1j
3pcbP00
P:301-536
1k
3pcbQ00
Q:301-536
1l
3pcbR00
R:301-536
[
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Pfam Domains
(0, 0)
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