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2QAA
Biol. Unit 3
Info
Asym.Unit (146 KB)
Biol.Unit 1 (72 KB)
Biol.Unit 2 (71 KB)
Biol.Unit 3, α-C (1.6 MB)
Biol.Unit 3 (1.6 MB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE SECOND TETRAHEDRAL INTERMEDIATES OF SGPB AT PH 7.3
Authors
:
T. W. Lee, M. N. G. James
Date
:
14 Jun 07 (Deposition) - 11 Dec 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.23
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (12x)
Keywords
:
Chymotrypsin-Type Serine Peptidase, Second Tetrahedral Intermediates, Single Amino Acids, Beta Barrels, Alpha Helix, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. W. Lee, M. N. James
1. 2A-Resolution Crystal Structures Reveal The Second Tetrahedral Intermediates Of Streptogrisin B (Sgpb).
Biochim. Biophys. Acta V. 1784 319 2008
[
close entry info
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Hetero Components
(7, 252)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
1c: ACETIC ACID (ACYc)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
2h: CHLORIDE ION (CLh)
2i: CHLORIDE ION (CLi)
2j: CHLORIDE ION (CLj)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
4a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
5d: GLYCEROL (GOLd)
6a: LEUCINE (LEUa)
6b: LEUCINE (LEUb)
7a: SULFATE ION (SO4a)
7b: SULFATE ION (SO4b)
7c: SULFATE ION (SO4c)
7d: SULFATE ION (SO4d)
7e: SULFATE ION (SO4e)
8a: TYROSINE (TYRa)
8b: TYROSINE (TYRb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
36
Ligand/Ion
ACETIC ACID
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
EDO
48
Ligand/Ion
1,2-ETHANEDIOL
4
EPE
12
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5
GOL
48
Ligand/Ion
GLYCEROL
6
LEU
24
Mod. Amino Acid
LEUCINE
7
SO4
60
Ligand/Ion
SULFATE ION
8
TYR
24
Mod. Amino Acid
TYROSINE
[
close Hetero Component info
]
Sites
(31, 31)
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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:163 , ARG A:182 , THR A:183 , ASN A:184 , THR A:225 , HOH A:1078 , HOH A:1136
BINDING SITE FOR RESIDUE SO4 A 912
02
AC2
SOFTWARE
ARG A:139 , THR A:157 , EDO A:921 , HOH A:1025 , HOH A:1230
BINDING SITE FOR RESIDUE SO4 A 913
03
AC3
SOFTWARE
GLY A:48C , EDO A:923
BINDING SITE FOR RESIDUE CL A 941
04
AC4
SOFTWARE
ARG A:41 , ACY A:931 , HOH A:1203
BINDING SITE FOR RESIDUE CL A 945
05
AC5
SOFTWARE
LYS A:115 , HOH A:1132 , HOH A:1213 , HOH A:1214
BINDING SITE FOR RESIDUE CL A 950
06
AC6
SOFTWARE
THR A:207 , ACY A:933 , HOH A:1238 , HOH A:1239 , ASN B:101 , HOH B:1186
BINDING SITE FOR RESIDUE CL A 957
07
AC7
SOFTWARE
THR B:163 , ARG B:182 , THR B:183 , ASN B:184 , THR B:225 , HOH B:1072 , HOH B:1081
BINDING SITE FOR RESIDUE SO4 B 911
08
AC8
SOFTWARE
HOH A:978 , ASN B:170 , GLY B:172 , GLY B:173 , HOH B:959 , HOH B:1181 , HOH B:1195
BINDING SITE FOR RESIDUE SO4 B 914
09
AC9
SOFTWARE
GLY A:174 , HOH A:975 , ARG B:139 , GLY B:156 , THR B:157 , GOL B:904 , HOH B:1116 , HOH B:1125 , HOH B:1197
BINDING SITE FOR RESIDUE SO4 B 915
10
BC1
SOFTWARE
SER B:79 , ARG B:81
BINDING SITE FOR RESIDUE CL B 942
11
BC2
SOFTWARE
ARG B:41 , HOH B:1050
BINDING SITE FOR RESIDUE CL B 943
12
BC3
SOFTWARE
ARG B:208 , HOH B:1006
BINDING SITE FOR RESIDUE CL B 944
13
BC4
SOFTWARE
THR A:39 , THR B:64 , THR B:65 , HOH B:1170
BINDING SITE FOR RESIDUE CL B 946
14
BC5
SOFTWARE
HIS B:158 , CYS B:220
BINDING SITE FOR RESIDUE CL B 952
15
BC6
SOFTWARE
SER B:89 , TYR B:237
BINDING SITE FOR RESIDUE CL B 954
16
BC7
SOFTWARE
HIS A:57 , ALA A:192 , GLU A:192A , PRO A:192B , GLY A:193 , SER A:195 , GLY A:216 , SER A:217 , GLY A:218 , GOL A:901 , HOH A:1046 , HOH A:1146 , HOH A:1165 , HOH A:1208 , HOH A:1232 , HOH A:1235
BINDING SITE FOR RESIDUE TYR A 1
17
BC8
SOFTWARE
HIS A:57 , GLU A:192A , PRO A:192B , GLY A:193 , SER A:195 , THR A:213 , SER A:214 , GLY A:215 , GOL A:901 , HOH A:1208 , HOH A:1232 , HOH A:1235
BINDING SITE FOR RESIDUE LEU A 2
18
BC9
SOFTWARE
GLY A:19 , ASP A:29 , ARG A:139 , GLY A:140 , SER A:141 , GLY A:156 , SO4 A:913 , HOH A:997
BINDING SITE FOR RESIDUE EDO A 921
19
CC1
SOFTWARE
SER A:33 , THR A:39 , GLY A:40 , CYS A:42 , CYS A:58
BINDING SITE FOR RESIDUE EDO A 922
20
CC2
SOFTWARE
ARG A:48A , THR A:125 , SER A:240 , VAL A:241 , TYR A:242 , CL A:941
BINDING SITE FOR RESIDUE EDO A 923
21
CC3
SOFTWARE
THR A:87 , ARG A:107 , HOH A:979 , SER B:126 , ALA B:127 , LEU B:235 , SER B:240 , VAL B:241 , ACY B:932 , HOH B:966 , HOH B:1087
BINDING SITE FOR RESIDUE EPE A 961
22
CC4
SOFTWARE
HIS B:57 , ALA B:192 , GLU B:192A , PRO B:192B , GLY B:193 , SER B:195 , SER B:214 , GLY B:215 , GLY B:216 , SER B:217 , GLY B:218 , GOL B:902 , HOH B:1013 , HOH B:1176 , HOH B:1177 , HOH B:1178 , HOH B:1192
BINDING SITE FOR RESIDUE TYR B 1
23
CC5
SOFTWARE
HIS B:57 , GLU B:192A , PRO B:192B , GLY B:193 , SER B:195 , THR B:213 , SER B:214 , GLY B:215 , GOL B:902 , HOH B:1178 , HOH B:1192
BINDING SITE FOR RESIDUE LEU B 2
24
CC6
SOFTWARE
ALA B:135 , VAL B:136 , THR B:137 , GLY B:202
BINDING SITE FOR RESIDUE EDO B 924
25
CC7
SOFTWARE
TYR A:1 , LEU A:2 , HIS A:57 , TYR A:171 , SER A:214 , GLY A:215 , HOH A:1194
BINDING SITE FOR RESIDUE GOL A 901
26
CC8
SOFTWARE
SER A:79 , ARG A:81 , CL A:945 , HOH A:1090 , HOH B:1009
BINDING SITE FOR RESIDUE ACY A 931
27
CC9
SOFTWARE
SER A:48D , GLN A:122 , GLY A:202 , THR A:207 , CL A:957 , HOH A:1105 , HOH A:1113 , ASN B:101 , GLU B:233 , HOH B:1004 , HOH B:1145
BINDING SITE FOR RESIDUE ACY A 933
28
DC1
SOFTWARE
TYR B:1 , LEU B:2 , TYR B:171 , SER B:214 , GLY B:215 , HOH B:1144 , HOH B:1163 , HOH B:1178
BINDING SITE FOR RESIDUE GOL B 902
29
DC2
SOFTWARE
SER A:48B , GLY A:238 , HOH A:970 , HOH A:983 , ASN B:166 , GLY B:179 , MET B:180 , PRO B:230 , HOH B:960 , HOH B:1030
BINDING SITE FOR RESIDUE GOL B 903
30
DC3
SOFTWARE
ASN A:100 , GLY A:174 , TYR A:178 , HOH A:1218 , GLY B:156 , THR B:157 , SO4 B:915 , HOH B:1101
BINDING SITE FOR RESIDUE GOL B 904
31
DC4
SOFTWARE
EPE A:961 , ARG B:48A , SER B:240 , HOH B:1070 , HOH B:1127 , HOH B:1175
BINDING SITE FOR RESIDUE ACY B 932
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 48)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_HIS (A:53-58,B:53-58)
2: TRYPSIN_SER (A:191-200,B:191-200)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
PRTB_STRGR
143-148
24
A:53-58
B:53-58
2
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
PRTB_STRGR
249-260
24
A:191-200
B:191-200
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
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_d2qaaa_ (A:)
1b: SCOP_d2qaab_ (B:)
View:
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Label:
Classes
(
)
(
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Folds
(
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(
)
Superfamilies
(
)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Trypsin-like serine proteases
(1752)
Superfamily
:
Trypsin-like serine proteases
(1752)
Family
:
Prokaryotic proteases
(131)
Protein domain
:
automated matches
(19)
Streptomyces griseus [TaxId: 1911]
(8)
1a
d2qaaa_
A:
1b
d2qaab_
B:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2qaaA02 (A:117-230)
1b: CATH_2qaaB02 (B:117-230)
1c: CATH_2qaaA01 (A:16-116,A:231-242)
1d: CATH_2qaaB01 (B:16-116,B:231-242)
View:
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Classes
(
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(
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Architectures
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
Streptomyces griseus. Organism_taxid: 1911
(4)
1a
2qaaA02
A:117-230
1b
2qaaB02
B:117-230
1c
2qaaA01
A:16-116,A:231-242
1d
2qaaB01
B:16-116,B:231-242
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Trypsin_2qaaB01 (B:16-236)
1b: PFAM_Trypsin_2qaaB02 (B:16-236)
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)
Organisms
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)
(
)
Clan
:
Peptidase_PA
(797)
Family
:
Trypsin
(679)
Streptomyces griseus
(24)
1a
Trypsin-2qaaB01
B:16-236
1b
Trypsin-2qaaB02
B:16-236
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Asymmetric Unit 1
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