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2J5N
Biol. Unit 1
Info
Asym.Unit (196 KB)
Biol.Unit 1 (563 KB)
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(1)
Title
:
1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS THERMOPHIRUS WITH BOUND INHIBITOR GLYCINE AND NAD.
Authors
:
E. Inagaki, K. Sakamoto, M. Nishio, S. Yokoyama
Date
:
19 Sep 06 (Deposition) - 16 Oct 07 (Release) - 29 Aug 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.63
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Glutamate, Type Ii Hyperprolinmia, Oxidoreductase, 1-Pyrroline-5-Carboxylate, Proline Methabolic Pathway
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Inagaki, K. Sakamoto, M. Nishio, S. Yokoyama, T. H. Tahirov
Crystal Structure Of Ternary Complex Of Delta1- Pyrroline-5-Carboxylate Dehydrogenase With Substrate Mimic And Co-Factoer
To Be Published
[
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Hetero Components
(5, 51)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
2a: GLYCINE (GLYa)
2b: GLYCINE (GLYb)
3a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
3b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
3c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
3d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
3e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
3f: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDf)
4a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
4b: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDb)
4c: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDc)
6a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
6b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
12
Ligand/Ion
ACETATE ION
2
GLY
6
Mod. Amino Acid
GLYCINE
3
MPD
18
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
MRD
9
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
5
NA
-1
Ligand/Ion
SODIUM ION
6
NAD
6
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
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Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:323 , GLY A:477 , ALA A:478 , PHE A:485 , HOH A:2246 , HOH A:2529 , HOH A:2541 , HOH A:2572
BINDING SITE FOR RESIDUE GLY A1517
02
AC2
SOFTWARE
ILE A:180 , ALA A:181 , PRO A:182 , TRP A:183 , ASN A:184 , ILE A:189 , LYS A:207 , ALA A:209 , GLU A:210 , GLY A:240 , GLU A:241 , GLY A:244 , ALA A:245 , PHE A:258 , THR A:259 , GLY A:260 , SER A:261 , VAL A:264 , GLU A:288 , THR A:289 , GLY A:290 , CYS A:322 , GLU A:417 , PHE A:419 , PHE A:485 , ACT A:1519 , HOH A:2323 , HOH A:2324 , HOH A:2573 , HOH A:2574 , HOH A:2575 , HOH A:2576 , HOH A:2577 , HOH A:2578 , HOH A:2579
BINDING SITE FOR RESIDUE NAD A1518
03
AC3
SOFTWARE
ALA A:245 , GLU A:249 , ALA A:271 , NAD A:1518 , HOH A:2580
BINDING SITE FOR RESIDUE ACT A1519
04
AC4
SOFTWARE
ARG A:462 , PHE A:464 , HIS A:465 , HOH A:2581 , HOH A:2582 , LYS B:510
BINDING SITE FOR RESIDUE ACT A1520
05
AC5
SOFTWARE
LEU A:275 , GLN A:279 , HOH A:2583 , HOH A:2584 , HOH A:2585
BINDING SITE FOR RESIDUE MRD A1521
06
AC6
SOFTWARE
PHE A:6 , TYR A:144 , ALA A:148 , HOH A:2262 , HOH A:2586 , HOH A:2587 , HOH A:2588 , GLU B:158
BINDING SITE FOR RESIDUE MPD A1522
07
AC7
SOFTWARE
ARG A:151 , TYR A:171 , HOH A:2269 , HOH A:2555 , HOH A:2589
BINDING SITE FOR RESIDUE MPD A1523
08
AC8
SOFTWARE
ARG A:36 , PRO A:39 , HOH A:2309
BINDING SITE FOR RESIDUE MPD A1524
09
AC9
SOFTWARE
SER A:55 , LEU A:56 , GLU A:123 , ASP A:211 , HOH A:2143 , HOH A:2426
BINDING SITE FOR RESIDUE NA A1525
10
BC1
SOFTWARE
SER B:323 , GLY B:477 , ALA B:478 , PHE B:485 , HOH B:2236 , HOH B:2377 , HOH B:2515 , HOH B:2556
BINDING SITE FOR RESIDUE GLY B1517
11
BC2
SOFTWARE
ILE B:180 , ALA B:181 , PRO B:182 , TRP B:183 , ASN B:184 , ILE B:189 , LYS B:207 , ALA B:209 , GLU B:210 , GLY B:240 , GLY B:244 , ALA B:245 , PHE B:258 , THR B:259 , GLY B:260 , SER B:261 , VAL B:264 , GLU B:288 , THR B:289 , GLY B:290 , CYS B:322 , GLU B:417 , PHE B:419 , LEU B:445 , PHE B:485 , ACT B:1519 , HOH B:2557 , HOH B:2558 , HOH B:2559 , HOH B:2560 , HOH B:2561 , HOH B:2562 , HOH B:2563
BINDING SITE FOR RESIDUE NAD B1518
12
BC3
SOFTWARE
ALA B:245 , GLU B:249 , ILE B:268 , ALA B:271 , NAD B:1518 , HOH B:2564
BINDING SITE FOR RESIDUE ACT B1519
13
BC4
SOFTWARE
LYS A:510 , ARG B:462 , PHE B:464 , HIS B:465 , HOH B:2565 , HOH B:2566
BINDING SITE FOR RESIDUE ACT B1520
14
BC5
SOFTWARE
ARG B:151 , HOH B:2540
BINDING SITE FOR RESIDUE MPD B1521
15
BC6
SOFTWARE
GLU A:158 , VAL A:160 , PHE B:6 , TYR B:144 , ALA B:148 , LEU B:500 , HOH B:2245 , HOH B:2567 , HOH B:2568 , HOH B:2569
BINDING SITE FOR RESIDUE MRD B1522
16
BC7
SOFTWARE
LEU B:275 , GLN B:279 , HOH B:2570 , HOH B:2571
BINDING SITE FOR RESIDUE MRD B1523
17
BC8
SOFTWARE
TYR B:38 , TRP B:46 , GLU B:221
BINDING SITE FOR RESIDUE MPD B1524
18
BC9
SOFTWARE
LEU A:27 , ARG A:28 , TYR A:122 , GLU A:355 , PRO B:353 , GLU B:355 , GLU B:356 , HOH B:2573 , HOH B:2574
BINDING SITE FOR RESIDUE MPD B1525
19
CC1
SOFTWARE
SER B:55 , LEU B:56 , GLU B:123 , ASP B:211 , HOH B:2132 , HOH B:2420
BINDING SITE FOR RESIDUE NA B1526
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
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Exons
(0, 0)
Info
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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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2j5na_ (A:)
1b: SCOP_d2j5nb_ (B:)
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Classes
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(
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(
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
ALDH-like
(168)
Superfamily
:
ALDH-like
(168)
Family
:
ALDH-like
(76)
Protein domain
:
automated matches
(24)
Thermus thermophilus HB8 [TaxId: 300852]
(15)
1a
d2j5na_
A:
1b
d2j5nb_
B:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2j5nA01 (A:1-289,A:480-516)
1b: CATH_2j5nB01 (B:1-289,B:480-516)
2a: CATH_2j5nA02 (A:290-479)
2b: CATH_2j5nB02 (B:290-479)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aldehyde Dehydrogenase; Chain A, domain 1
(86)
Homologous Superfamily
:
Aldehyde Dehydrogenase; Chain A, domain 1
(86)
Thermus thermophilus. Organism_taxid: 300852. Strain: hb8.
(8)
1a
2j5nA01
A:1-289,A:480-516
1b
2j5nB01
B:1-289,B:480-516
Topology
:
Aldehyde Dehydrogenase; Chain A, domain 2
(89)
Homologous Superfamily
:
Aldehyde Dehydrogenase; Chain A, domain 2
(89)
Thermus thermophilus. Organism_taxid: 300852. Strain: hb8.
(8)
2a
2j5nA02
A:290-479
2b
2j5nB02
B:290-479
[
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Pfam Domains
(0, 0)
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all PFAM domains
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