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2EII
Asym. Unit
Info
Asym.Unit (195 KB)
Biol.Unit 1 (189 KB)
Biol.Unit 2 (559 KB)
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(1)
Title
:
CRYSTAL ANALYSIS OF DELTA1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS THERMOPHILUS WITH BOUND L-VALINE AND NAD.
Authors
:
E. Inagaki, K. Sakamoto, S. Yokoyama, Riken Structural Genomics/Pr Initiative (Rsgi)
Date
:
13 Mar 07 (Deposition) - 18 Sep 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.88
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (3x)
Keywords
:
Enzyme-Coenzyme-Inhibitor Ternary Complex, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase
(Keyword Search:
[
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)
Reference
:
E. Inagaki, N. Ohshima, K. Sakamoto, H. Kato, S. Yokoyama, T. H. Tahiro
Crystal Structure Analysis Of Delta1-Pyrroline-5-Carboxylat Dehydrogenase In Ternary Complex With Inhibitor And Nad.
To Be Published
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Hetero Components
(5, 24)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
2c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
2d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
2e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
2f: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDf)
2g: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDg)
2h: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDh)
2i: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDi)
2j: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDj)
2k: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDk)
2l: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDl)
2m: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDm)
2n: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDn)
4a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
4b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
5a: VALINE (VALa)
5b: VALINE (VALb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
4
Ligand/Ion
ACETATE ION
2
MPD
14
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
NA
2
Ligand/Ion
SODIUM ION
4
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
5
VAL
2
Mod. Amino Acid
VALINE
[
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Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:245 , GLU A:249 , ILE A:268 , ALA A:271 , NAD A:1518 , HOH A:2863
BINDING SITE FOR RESIDUE ACT A 1519
02
AC2
SOFTWARE
ARG A:462 , PHE A:464 , HIS A:465 , HOH A:2790 , LYS B:510
BINDING SITE FOR RESIDUE ACT A 1520
03
AC3
SOFTWARE
SER A:55 , LEU A:56 , GLU A:123 , ASP A:211 , HOH A:2701 , HOH A:2813
BINDING SITE FOR RESIDUE NA A 1540
04
AC4
SOFTWARE
ALA B:245 , GLU B:249 , ILE B:268 , ALA B:271 , NAD B:2518 , HOH B:2979
BINDING SITE FOR RESIDUE ACT B 2519
05
AC5
SOFTWARE
LYS A:510 , ARG B:462 , PHE B:464 , HIS B:465 , HOH B:2749 , HOH B:2829
BINDING SITE FOR RESIDUE ACT B 2520
06
AC6
SOFTWARE
SER B:55 , LEU B:56 , GLU B:123 , ASP B:211 , HOH B:2857 , HOH B:2872
BINDING SITE FOR RESIDUE NA B 2540
07
AC7
SOFTWARE
GLU A:137 , PHE A:185 , CYS A:322 , SER A:323 , GLY A:477 , ALA A:478 , PHE A:485 , HOH A:2563 , HOH A:2660 , HOH A:3025 , HOH A:3026
BINDING SITE FOR RESIDUE VAL A 1517
08
AC8
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 , LEU A:445 , PHE A:485 , ACT A:1519 , HOH A:2639 , HOH A:2828 , HOH A:2845 , HOH A:2862 , HOH A:3002 , HOH A:3031 , HOH A:3032 , HOH A:3034
BINDING SITE FOR RESIDUE NAD A 1518
09
AC9
SOFTWARE
GLU B:137 , PHE B:185 , SER B:323 , GLY B:477 , ALA B:478 , PHE B:485 , HOH B:2582 , HOH B:2664 , HOH B:3007 , HOH B:3008
BINDING SITE FOR RESIDUE VAL B 2517
10
BC1
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:2519 , HOH B:2650 , HOH B:2653 , HOH B:2767 , HOH B:2768 , HOH B:2847 , HOH B:3006
BINDING SITE FOR RESIDUE NAD B 2518
11
BC2
SOFTWARE
GLU A:158 , PHE B:6 , TYR B:144 , ALA B:148 , HOH B:2604 , HOH B:2616 , HOH B:2655 , HOH B:2866
BINDING SITE FOR RESIDUE MPD B 1530
12
BC3
SOFTWARE
ASP A:359 , HOH A:2607
BINDING SITE FOR RESIDUE MPD A 1531
13
BC4
SOFTWARE
LEU A:275 , GLN A:279 , HOH A:2706 , HOH A:2999 , MPD B:2535
BINDING SITE FOR RESIDUE MPD A 1532
14
BC5
SOFTWARE
TYR A:171 , HOH B:2810
BINDING SITE FOR RESIDUE MPD A 1533
15
BC6
SOFTWARE
LEU B:275 , GLN B:279 , HOH B:2733 , HOH B:2913
BINDING SITE FOR RESIDUE MPD B 1534
16
BC7
SOFTWARE
PHE A:170 , PRO B:94 , ARG B:462 , HOH B:2732 , HOH B:2997
BINDING SITE FOR RESIDUE MPD B 1535
17
BC8
SOFTWARE
ARG A:36 , TYR A:38 , PRO A:39 , TRP A:46
BINDING SITE FOR RESIDUE MPD A 1536
18
BC9
SOFTWARE
PHE A:6 , TYR A:144 , ALA A:148 , HOH A:2614 , HOH A:2622 , HOH A:2749 , GLU B:158
BINDING SITE FOR RESIDUE MPD A 2530
19
CC1
SOFTWARE
ARG B:36 , GLU B:221
BINDING SITE FOR RESIDUE MPD B 2531
20
CC2
SOFTWARE
LEU A:27 , ARG A:28 , TYR A:122 , GLU A:355 , PRO B:353 , GLU B:355 , GLU B:356 , HOH B:2659 , HOH B:2898
BINDING SITE FOR RESIDUE MPD B 2532
21
CC3
SOFTWARE
PRO A:94 , ARG A:462 , HOH A:2694 , HOH A:2848 , TYR B:154 , PHE B:170
BINDING SITE FOR RESIDUE MPD B 2533
22
CC4
SOFTWARE
ARG B:151
BINDING SITE FOR RESIDUE MPD B 2534
23
CC5
SOFTWARE
MPD A:1532 , GLU B:416 , HOH B:2565 , HOH B:2722
BINDING SITE FOR RESIDUE MPD B 2535
24
CC6
SOFTWARE
VAL B:312 , TYR B:315 , GLY B:316 , ASP B:359 , HOH B:2651
BINDING SITE FOR RESIDUE MPD B 2536
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
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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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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2eiia_ (A:)
1b: SCOP_d2eiib_ (B:)
View:
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Classes
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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
d2eiia_
A:
1b
d2eiib_
B:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2eiiA01 (A:1-289,A:480-516)
1b: CATH_2eiiB01 (B:1-289,B:480-516)
2a: CATH_2eiiA02 (A:290-479)
2b: CATH_2eiiB02 (B:290-479)
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Topologies
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Homologous Superfamilies
(
)
(
)
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 hb8. Organism_taxid: 300852. Strain: hb8.
(9)
1a
2eiiA01
A:1-289,A:480-516
1b
2eiiB01
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 hb8. Organism_taxid: 300852. Strain: hb8.
(9)
2a
2eiiA02
A:290-479
2b
2eiiB02
B:290-479
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (195 KB)
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