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3N25
Biol. Unit 1
Info
Asym.Unit (672 KB)
Biol.Unit 1 (336 KB)
Biol.Unit 2 (331 KB)
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(1)
Title
:
THE STRUCTURE OF MUSCLE PYRUVATE KINASE IN COMPLEX WITH PROLINE, PYRUVATE, AND MN2+
Authors
:
A. W. Fenton, T. A. Johnson, T. Holyoak
Date
:
17 May 10 (Deposition) - 28 Jul 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.41
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
:
Pyruvate Kinase, Glycolysis, Allosteric Regulation, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. W. Fenton, T. A. Johnson, T. Holyoak
The Pyruvate Kinase Model System, A Cautionary Tale For The Use Of Osmolyte Perturbations To Support Conformational Equilibria In Allostery.
Protein Sci. V. 19 1796 2010
[
close entry info
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Hetero Components
(4, 28)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
1n: 1,2-ETHANEDIOL (EDOn)
1o: 1,2-ETHANEDIOL (EDOo)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
2s: GLYCEROL (GOLs)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
3c: POTASSIUM ION (Kc)
3d: POTASSIUM ION (Kd)
3e: POTASSIUM ION (Ke)
3f: POTASSIUM ION (Kf)
3g: POTASSIUM ION (Kg)
3h: POTASSIUM ION (Kh)
4a: MANGANESE (II) ION (MNa)
4b: MANGANESE (II) ION (MNb)
4c: MANGANESE (II) ION (MNc)
4d: MANGANESE (II) ION (MNd)
4e: MANGANESE (II) ION (MNe)
4f: MANGANESE (II) ION (MNf)
4g: MANGANESE (II) ION (MNg)
4h: MANGANESE (II) ION (MNh)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
5d: SODIUM ION (NAd)
5e: SODIUM ION (NAe)
5f: SODIUM ION (NAf)
5g: SODIUM ION (NAg)
5h: SODIUM ION (NAh)
5i: SODIUM ION (NAi)
5j: SODIUM ION (NAj)
5k: SODIUM ION (NAk)
5l: SODIUM ION (NAl)
6a: PROLINE (PROa)
6b: PROLINE (PROb)
6c: PROLINE (PROc)
6d: PROLINE (PROd)
6e: PROLINE (PROe)
6f: PROLINE (PROf)
6g: PROLINE (PROg)
6h: PROLINE (PROh)
7a: PYRUVIC ACID (PYRa)
7b: PYRUVIC ACID (PYRb)
7c: PYRUVIC ACID (PYRc)
7d: PYRUVIC ACID (PYRd)
7e: PYRUVIC ACID (PYRe)
7f: PYRUVIC ACID (PYRf)
7g: PYRUVIC ACID (PYRg)
7h: PYRUVIC ACID (PYRh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
9
Ligand/Ion
1,2-ETHANEDIOL
2
GOL
11
Ligand/Ion
GLYCEROL
3
K
-1
Ligand/Ion
POTASSIUM ION
4
MN
-1
Ligand/Ion
MANGANESE (II) ION
5
NA
-1
Ligand/Ion
SODIUM ION
6
PRO
4
Mod. Amino Acid
PROLINE
7
PYR
4
Ligand/Ion
PYRUVIC ACID
[
close Hetero Component info
]
Sites
(42, 42)
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)
11: BC6 (SOFTWARE)
12: BC7 (SOFTWARE)
13: BC8 (SOFTWARE)
14: BC9 (SOFTWARE)
15: CC1 (SOFTWARE)
16: CC2 (SOFTWARE)
17: CC3 (SOFTWARE)
18: CC4 (SOFTWARE)
19: CC5 (SOFTWARE)
20: CC6 (SOFTWARE)
21: CC7 (SOFTWARE)
22: CC8 (SOFTWARE)
23: CC9 (SOFTWARE)
24: DC1 (SOFTWARE)
25: DC2 (SOFTWARE)
26: DC3 (SOFTWARE)
27: DC4 (SOFTWARE)
28: DC5 (SOFTWARE)
29: DC6 (SOFTWARE)
30: DC7 (SOFTWARE)
31: DC8 (SOFTWARE)
32: DC9 (SOFTWARE)
33: EC1 (SOFTWARE)
34: EC2 (SOFTWARE)
35: EC3 (SOFTWARE)
36: EC4 (SOFTWARE)
37: EC5 (SOFTWARE)
38: EC6 (SOFTWARE)
39: EC7 (SOFTWARE)
40: EC8 (SOFTWARE)
41: EC9 (SOFTWARE)
42: FC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:42 , ASN A:43 , ASN A:69 , ARG A:105 , HIS A:463 , TYR A:465 , ILE A:468 , PHE A:469 , PRO A:470 , HOH A:1265
BINDING SITE FOR RESIDUE PRO A 1200
02
AC2
SOFTWARE
ARG B:42 , ASN B:43 , ASN B:69 , HIS B:463 , ILE B:468 , PHE B:469 , PRO B:470 , HOH B:769
BINDING SITE FOR RESIDUE PRO B 1600
03
AC3
SOFTWARE
ARG C:42 , ASN C:43 , GLY C:45 , ASN C:69 , ARG C:105 , HIS C:463 , ILE C:468 , PHE C:469 , PRO C:470 , HOH C:1638
BINDING SITE FOR RESIDUE PRO C 1600
04
AC4
SOFTWARE
ARG D:42 , ASN D:43 , ASN D:69 , ARG D:105 , HIS D:463 , ILE D:468 , PHE D:469 , PRO D:470 , HOH D:1419
BINDING SITE FOR RESIDUE PRO D 1600
05
AC9
SOFTWARE
GLU A:271 , ASP A:295 , PYR A:1000 , HOH A:1225 , HOH A:1275
BINDING SITE FOR RESIDUE MN A 640
06
BC1
SOFTWARE
ARG A:72 , LYS A:269 , GLU A:271 , ALA A:292 , ARG A:293 , GLY A:294 , ASP A:295 , THR A:327 , MN A:640 , HOH A:1214 , HOH A:1225 , HOH A:1275
BINDING SITE FOR RESIDUE PYR A 1000
07
BC2
SOFTWARE
ASN A:74 , SER A:76 , ASP A:112 , THR A:113 , HOH A:765 , HOH A:1069
BINDING SITE FOR RESIDUE K A 1100
08
BC3
SOFTWARE
LYS A:124 , GLY A:125 , SER A:126 , GLY A:127 , THR A:128 , HOH A:1392
BINDING SITE FOR RESIDUE NA A 1300
09
BC4
SOFTWARE
THR A:431 , SER A:433 , SER A:436
BINDING SITE FOR RESIDUE NA A 2100
10
BC5
SOFTWARE
ARG A:42 , LYS A:65 , SER A:66 , GLY A:67 , HIS A:378
BINDING SITE FOR RESIDUE GOL A 6002
11
BC6
SOFTWARE
GLU A:95 , TYR A:104 , HIS A:456
BINDING SITE FOR RESIDUE EDO A 6043
12
BC7
SOFTWARE
GLU A:284 , ALA A:285 , SER A:286 , ASP A:287 , LYS A:321
BINDING SITE FOR RESIDUE EDO A 6050
13
BC8
SOFTWARE
ARG A:338 , PRO A:339 , ARG A:341 , HOH A:655 , ASP C:177 , GLN C:328
BINDING SITE FOR RESIDUE EDO A 6051
14
BC9
SOFTWARE
PRO A:116 , ASN A:209 , LEU A:210 , VAL A:215 , PHE A:243 , ARG A:245 , GLU A:299 , GOL A:6301
BINDING SITE FOR RESIDUE GOL A 6201
15
CC1
SOFTWARE
GLU A:117 , ILE A:118 , GLY A:207 , VAL A:208 , PHE A:243 , ASP A:295 , GOL A:6201
BINDING SITE FOR RESIDUE GOL A 6301
16
CC2
SOFTWARE
GLU B:271 , ASP B:295 , HOH B:1195 , PYR B:1500 , HOH B:1630
BINDING SITE FOR RESIDUE MN B 640
17
CC3
SOFTWARE
ARG B:72 , LYS B:269 , GLU B:271 , ALA B:292 , ARG B:293 , GLY B:294 , ASP B:295 , THR B:327 , MN B:640 , HOH B:1195 , HOH B:1604 , HOH B:1630 , EDO B:6048
BINDING SITE FOR RESIDUE PYR B 1500
18
CC4
SOFTWARE
ASN B:74 , SER B:76 , ASP B:112 , THR B:113 , SER B:242
BINDING SITE FOR RESIDUE K B 1700
19
CC5
SOFTWARE
SER B:436 , HOH B:1602
BINDING SITE FOR RESIDUE NA B 2000
20
CC6
SOFTWARE
LYS B:65 , SER B:66 , HIS B:378
BINDING SITE FOR RESIDUE GOL B 6007
21
CC7
SOFTWARE
ALA B:37 , PRO B:38
BINDING SITE FOR RESIDUE EDO B 6013
22
CC8
SOFTWARE
ASP B:177 , ASP B:295 , ILE B:298 , HOH B:1195 , PYR B:1500
BINDING SITE FOR RESIDUE EDO B 6048
23
CC9
SOFTWARE
PRO B:116 , ASN B:209 , LEU B:210 , VAL B:215 , PHE B:243 , ARG B:245 , GLU B:299
BINDING SITE FOR RESIDUE GOL B 6202
24
DC1
SOFTWARE
GLU B:117 , ILE B:118 , GLY B:207 , VAL B:208 , PHE B:243 , ASP B:295 , HOH B:1232
BINDING SITE FOR RESIDUE GOL B 6302
25
DC2
SOFTWARE
GLU C:271 , ASP C:295 , HOH C:1196 , PYR C:1500 , HOH C:1614
BINDING SITE FOR RESIDUE MN C 640
26
DC3
SOFTWARE
LYS C:269 , GLU C:271 , ALA C:292 , ARG C:293 , GLY C:294 , ASP C:295 , THR C:327 , MN C:640 , HOH C:1614
BINDING SITE FOR RESIDUE PYR C 1500
27
DC4
SOFTWARE
ASN C:74 , SER C:76 , ASP C:112 , THR C:113 , SER C:242 , HOH C:1097
BINDING SITE FOR RESIDUE K C 1700
28
DC5
SOFTWARE
THR C:431 , SER C:433 , SER C:436 , HOH C:1263
BINDING SITE FOR RESIDUE NA C 2000
29
DC6
SOFTWARE
ALA C:37 , PRO C:38 , THR C:40
BINDING SITE FOR RESIDUE EDO C 6014
30
DC7
SOFTWARE
PHE C:97 , LEU C:103 , ARG C:105 , ARG C:499
BINDING SITE FOR RESIDUE GOL C 6055
31
DC8
SOFTWARE
GLU C:117 , ILE C:118 , GLY C:207 , VAL C:208 , PHE C:243 , ASP C:295
BINDING SITE FOR RESIDUE GOL C 6303
32
DC9
SOFTWARE
ARG C:391 , ALA D:398 , ARG D:399 , SER D:402 , HOH D:1038 , HOH D:1610
BINDING SITE FOR RESIDUE GOL D 6056
33
EC1
SOFTWARE
GLU D:271 , ASP D:295 , HOH D:1274 , PYR D:1500
BINDING SITE FOR RESIDUE MN D 640
34
EC2
SOFTWARE
LYS D:269 , GLU D:271 , ALA D:292 , ARG D:293 , GLY D:294 , ASP D:295 , THR D:327 , MN D:640 , HOH D:1274 , HOH D:1625 , EDO D:6033
BINDING SITE FOR RESIDUE PYR D 1500
35
EC3
SOFTWARE
ASN D:74 , SER D:76 , ASP D:112 , THR D:113 , SER D:242
BINDING SITE FOR RESIDUE K D 1700
36
EC4
SOFTWARE
LYS D:124 , GLY D:125 , THR D:128 , HOH D:1394
BINDING SITE FOR RESIDUE NA D 2000
37
EC5
SOFTWARE
THR D:431 , SER D:433 , SER D:436 , HOH D:1395
BINDING SITE FOR RESIDUE NA D 2100
38
EC6
SOFTWARE
PRO D:38 , THR D:40
BINDING SITE FOR RESIDUE EDO D 6011
39
EC7
SOFTWARE
THR D:49 , ARG D:72 , ASN D:74 , ALA D:365
BINDING SITE FOR RESIDUE EDO D 6017
40
EC8
SOFTWARE
ASP D:177 , PYR D:1500
BINDING SITE FOR RESIDUE EDO D 6033
41
EC9
SOFTWARE
PRO D:116 , ASN D:209 , LEU D:210 , VAL D:215 , ARG D:245 , GLU D:299
BINDING SITE FOR RESIDUE GOL D 6204
42
FC1
SOFTWARE
GLU D:117 , ILE D:118 , VAL D:208 , PHE D:243 , ASP D:295
BINDING SITE FOR RESIDUE GOL D 6304
[
close Site info
]
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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: PYRUVATE_KINASE (A:264-276,B:264-276,C:264-276,D:26...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PYRUVATE_KINASE
PS00110
Pyruvate kinase active site signature.
KPYM_RABIT
265-277
4
A:264-276
B:264-276
C:264-276
D:264-276
-
-
-
-
[
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]
Exons
(0, 0)
Info
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
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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_PK_3n25H01 (H:41-394)
1b: PFAM_PK_3n25H02 (H:41-394)
1c: PFAM_PK_3n25H03 (H:41-394)
1d: PFAM_PK_3n25H04 (H:41-394)
1e: PFAM_PK_3n25H05 (H:41-394)
1f: PFAM_PK_3n25H06 (H:41-394)
1g: PFAM_PK_3n25H07 (H:41-394)
1h: PFAM_PK_3n25H08 (H:41-394)
2a: PFAM_PK_C_3n25H09 (H:408-528)
2b: PFAM_PK_C_3n25H10 (H:408-528)
2c: PFAM_PK_C_3n25H11 (H:408-528)
2d: PFAM_PK_C_3n25H12 (H:408-528)
2e: PFAM_PK_C_3n25H13 (H:408-528)
2f: PFAM_PK_C_3n25H14 (H:408-528)
2g: PFAM_PK_C_3n25H15 (H:408-528)
2h: PFAM_PK_C_3n25H16 (H:408-528)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PK_TIM
(63)
Family
:
PK
(17)
Oryctolagus cuniculus (Rabbit)
(2)
1a
PK-3n25H01
H:41-394
1b
PK-3n25H02
H:41-394
1c
PK-3n25H03
H:41-394
1d
PK-3n25H04
H:41-394
1e
PK-3n25H05
H:41-394
1f
PK-3n25H06
H:41-394
1g
PK-3n25H07
H:41-394
1h
PK-3n25H08
H:41-394
Clan
:
no clan defined [family: PK_C]
(19)
Family
:
PK_C
(19)
Oryctolagus cuniculus (Rabbit)
(2)
2a
PK_C-3n25H09
H:408-528
2b
PK_C-3n25H10
H:408-528
2c
PK_C-3n25H11
H:408-528
2d
PK_C-3n25H12
H:408-528
2e
PK_C-3n25H13
H:408-528
2f
PK_C-3n25H14
H:408-528
2g
PK_C-3n25H15
H:408-528
2h
PK_C-3n25H16
H:408-528
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