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1UP7
Biol. Unit 1
Info
Asym.Unit (565 KB)
Biol.Unit 1 (283 KB)
Biol.Unit 2 (278 KB)
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(1)
Title
:
STRUCTURE OF THE 6-PHOSPHO-BETA GLUCOSIDASE FROM THERMOTOGA MARITIMA AT 2.4 ANGSTROM RESOLUTION IN THE TETRAGONAL FORM WITH NAD AND GLUCOSE-6-PHOSPHATE
Authors
:
A. Varrot, V. L. Yip, S. G. Withers, G. J. Davies
Date
:
29 Sep 03 (Deposition) - 18 Nov 04 (Release) - 28 Dec 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Hydrolase, 6-Phospho-Beta-Glucosidase, Family4 Hydrolase, Nad Dependent
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Varrot, V. L. Yip, Y. Li, S. S. Rajan, X. Yang, W. F. Anderson, J. Thompson, S. G. Withers, G. J. Davies
Nad+ And Metal-Ion Dependent Hydrolysis By Family 4 Glycosidases: Structural Insight Into Specificity For Phospho-Beta-D-Glucosides
J. Mol. Biol. V. 346 423 2005
[
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Hetero Components
(3, 10)
Info
All Hetero Components
1a: ALPHA-D-GLUCOSE-6-PHOSPHATE (G6Pa)
1b: ALPHA-D-GLUCOSE-6-PHOSPHATE (G6Pb)
1c: ALPHA-D-GLUCOSE-6-PHOSPHATE (G6Pc)
1d: ALPHA-D-GLUCOSE-6-PHOSPHATE (G6Pd)
1e: ALPHA-D-GLUCOSE-6-PHOSPHATE (G6Pe)
1f: ALPHA-D-GLUCOSE-6-PHOSPHATE (G6Pf)
1g: ALPHA-D-GLUCOSE-6-PHOSPHATE (G6Pg)
1h: ALPHA-D-GLUCOSE-6-PHOSPHATE (G6Ph)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
2d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
2e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
2f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
2g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
2h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
G6P
4
Ligand/Ion
ALPHA-D-GLUCOSE-6-PHOSPHATE
2
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
SO4
2
Ligand/Ion
SULFATE ION
[
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:12 , ARG A:87 , GLU A:103 , ASN A:140 , ASN A:163 , HIS A:192 , TYR A:241 , ARG A:261 , VAL A:265 , ARG A:289 , GLY A:290 , TYR A:294 , NAD A:1416
BINDING SITE FOR RESIDUE G6P A1417
02
AC2
SOFTWARE
ARG B:87 , GLU B:103 , ASN B:140 , ASN B:163 , VAL B:164 , HIS B:192 , TYR B:241 , ARG B:261 , ARG B:289 , GLY B:290 , TYR B:294 , NAD B:1416
BINDING SITE FOR RESIDUE G6P B1417
03
AC3
SOFTWARE
TYR C:12 , ARG C:87 , GLU C:103 , ASN C:140 , ASN C:163 , HIS C:192 , TYR C:241 , ARG C:261 , VAL C:265 , ARG C:289 , GLY C:290 , TYR C:294 , NAD C:1416
BINDING SITE FOR RESIDUE G6P C1417
04
AC4
SOFTWARE
TYR D:12 , ARG D:87 , GLU D:103 , ASN D:140 , CYS D:162 , ASN D:163 , VAL D:164 , HIS D:192 , TYR D:241 , ARG D:261 , VAL D:265 , ARG D:289 , GLY D:290 , GLY D:291 , TYR D:294 , NAD D:1416
BINDING SITE FOR RESIDUE G6P D1417
05
AC9
SOFTWARE
ASP A:393 , HOH A:2149 , GLU B:248
BINDING SITE FOR RESIDUE SO4 A1418
06
BC1
SOFTWARE
GLU C:248 , PRO C:389 , GLY C:391 , HOH D:2041
BINDING SITE FOR RESIDUE SO4 C1418
07
BC2
SOFTWARE
GLY A:9 , SER A:10 , TYR A:12 , ASP A:36 , ILE A:37 , LYS A:41 , GLN A:78 , PHE A:79 , ARG A:80 , GLU A:103 , TYR A:123 , PHE A:138 , ASN A:140 , GLU A:269 , ARG A:289 , GLY A:291 , TYR A:294 , G6P A:1417 , HOH A:2095 , HOH A:2145 , HOH A:2146 , HOH A:2147 , HOH A:2148
BINDING SITE FOR RESIDUE NAD A1416
08
BC3
SOFTWARE
GLY B:7 , GLY B:9 , SER B:10 , TYR B:12 , ASP B:36 , ILE B:37 , ASP B:38 , LYS B:41 , GLN B:78 , PHE B:79 , ARG B:80 , GLU B:103 , ILE B:119 , TYR B:123 , PHE B:138 , ASN B:140 , GLU B:269 , ARG B:289 , TYR B:294 , G6P B:1417 , HOH B:2009
BINDING SITE FOR RESIDUE NAD B1416
09
BC4
SOFTWARE
GLY C:9 , SER C:10 , TYR C:12 , ASP C:36 , ILE C:37 , LYS C:41 , GLN C:78 , PHE C:79 , ARG C:80 , GLU C:103 , TYR C:123 , PHE C:138 , THR C:139 , ASN C:140 , GLU C:269 , ARG C:289 , TYR C:294 , G6P C:1417 , HOH C:2106 , HOH C:2107
BINDING SITE FOR RESIDUE NAD C1416
10
BC5
SOFTWARE
GLY D:7 , GLY D:9 , SER D:10 , TYR D:12 , TYR D:35 , ASP D:36 , ILE D:37 , ASP D:38 , LYS D:41 , GLN D:78 , PHE D:79 , ARG D:80 , GLU D:103 , ILE D:119 , TYR D:123 , PHE D:138 , ASN D:140 , GLY D:291 , TYR D:294 , SER D:295 , G6P D:1417 , HOH D:2091
BINDING SITE FOR RESIDUE NAD D1416
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GLYCOSYL_HYDROL_F4 (A:131-162,B:131-162,C:131-162,D:13...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLYCOSYL_HYDROL_F4
PS01324
Glycosyl hydrolases family 4 signature.
BGLT_THEMA
131-162
4
A:131-162
B:131-162
C:131-162
D:131-162
-
-
-
-
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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
(2, 16)
Info
All SCOP Domains
1a: SCOP_d1up7a2 (A:163-415)
1b: SCOP_d1up7b2 (B:163-415)
1c: SCOP_d1up7c2 (C:163-415)
1d: SCOP_d1up7d2 (D:163-415)
1e: SCOP_d1up7e2 (E:163-415)
1f: SCOP_d1up7f2 (F:163-415)
1g: SCOP_d1up7g2 (G:163-415)
1h: SCOP_d1up7h2 (H:163-415)
2a: SCOP_d1up7a1 (A:1-162)
2b: SCOP_d1up7b1 (B:1-162)
2c: SCOP_d1up7c1 (C:1-162)
2d: SCOP_d1up7d1 (D:1-162)
2e: SCOP_d1up7e1 (E:1-162)
2f: SCOP_d1up7f1 (F:1-162)
2g: SCOP_d1up7g1 (G:1-162)
2h: SCOP_d1up7h1 (H:1-162)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
LDH C-terminal domain-like
(172)
Superfamily
:
LDH C-terminal domain-like
(172)
Family
:
AglA-like glucosidase
(9)
Protein domain
:
6-phospho-beta-glucosidase
(4)
Thermotoga maritima [TaxId: 2336]
(3)
1a
d1up7a2
A:163-415
1b
d1up7b2
B:163-415
1c
d1up7c2
C:163-415
1d
d1up7d2
D:163-415
1e
d1up7e2
E:163-415
1f
d1up7f2
F:163-415
1g
d1up7g2
G:163-415
1h
d1up7h2
H:163-415
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
LDH N-terminal domain-like
(117)
Protein domain
:
6-phospho-beta-glucosidase
(4)
Thermotoga maritima [TaxId: 2336]
(3)
2a
d1up7a1
A:1-162
2b
d1up7b1
B:1-162
2c
d1up7c1
C:1-162
2d
d1up7d1
D:1-162
2e
d1up7e1
E:1-162
2f
d1up7f1
F:1-162
2g
d1up7g1
G:1-162
2h
d1up7h1
H:1-162
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(2, 16)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_4C_1up7H01 (H:181-391)
1b: PFAM_Glyco_hydro_4C_1up7H02 (H:181-391)
1c: PFAM_Glyco_hydro_4C_1up7H03 (H:181-391)
1d: PFAM_Glyco_hydro_4C_1up7H04 (H:181-391)
1e: PFAM_Glyco_hydro_4C_1up7H05 (H:181-391)
1f: PFAM_Glyco_hydro_4C_1up7H06 (H:181-391)
1g: PFAM_Glyco_hydro_4C_1up7H07 (H:181-391)
1h: PFAM_Glyco_hydro_4C_1up7H08 (H:181-391)
2a: PFAM_Glyco_hydro_4_1up7H09 (H:2-178)
2b: PFAM_Glyco_hydro_4_1up7H10 (H:2-178)
2c: PFAM_Glyco_hydro_4_1up7H11 (H:2-178)
2d: PFAM_Glyco_hydro_4_1up7H12 (H:2-178)
2e: PFAM_Glyco_hydro_4_1up7H13 (H:2-178)
2f: PFAM_Glyco_hydro_4_1up7H14 (H:2-178)
2g: PFAM_Glyco_hydro_4_1up7H15 (H:2-178)
2h: PFAM_Glyco_hydro_4_1up7H16 (H:2-178)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
LDH_C
(56)
Family
:
Glyco_hydro_4C
(5)
Thermotoga maritima
(4)
1a
Glyco_hydro_4C-1up7H01
H:181-391
1b
Glyco_hydro_4C-1up7H02
H:181-391
1c
Glyco_hydro_4C-1up7H03
H:181-391
1d
Glyco_hydro_4C-1up7H04
H:181-391
1e
Glyco_hydro_4C-1up7H05
H:181-391
1f
Glyco_hydro_4C-1up7H06
H:181-391
1g
Glyco_hydro_4C-1up7H07
H:181-391
1h
Glyco_hydro_4C-1up7H08
H:181-391
Clan
:
NADP_Rossmann
(1239)
Family
:
Glyco_hydro_4
(5)
Thermotoga maritima
(4)
2a
Glyco_hydro_4-1up7H09
H:2-178
2b
Glyco_hydro_4-1up7H10
H:2-178
2c
Glyco_hydro_4-1up7H11
H:2-178
2d
Glyco_hydro_4-1up7H12
H:2-178
2e
Glyco_hydro_4-1up7H13
H:2-178
2f
Glyco_hydro_4-1up7H14
H:2-178
2g
Glyco_hydro_4-1up7H15
H:2-178
2h
Glyco_hydro_4-1up7H16
H:2-178
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