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3N25
Biol. Unit 2
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, 22)
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
6
Ligand/Ion
1,2-ETHANEDIOL
2
GOL
8
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
(36, 36)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: FC2 (SOFTWARE)
06: FC3 (SOFTWARE)
07: FC4 (SOFTWARE)
08: FC5 (SOFTWARE)
09: FC6 (SOFTWARE)
10: FC7 (SOFTWARE)
11: FC8 (SOFTWARE)
12: FC9 (SOFTWARE)
13: GC1 (SOFTWARE)
14: GC2 (SOFTWARE)
15: GC3 (SOFTWARE)
16: GC4 (SOFTWARE)
17: GC5 (SOFTWARE)
18: GC6 (SOFTWARE)
19: GC7 (SOFTWARE)
20: GC8 (SOFTWARE)
21: GC9 (SOFTWARE)
22: HC1 (SOFTWARE)
23: HC2 (SOFTWARE)
24: HC3 (SOFTWARE)
25: HC4 (SOFTWARE)
26: HC5 (SOFTWARE)
27: HC6 (SOFTWARE)
28: HC7 (SOFTWARE)
29: HC8 (SOFTWARE)
30: HC9 (SOFTWARE)
31: IC1 (SOFTWARE)
32: IC2 (SOFTWARE)
33: IC3 (SOFTWARE)
34: IC4 (SOFTWARE)
35: IC5 (SOFTWARE)
36: IC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
ARG E:42 , ASN E:43 , ASN E:69 , ARG E:105 , HIS E:463 , ILE E:468 , PHE E:469 , PRO E:470 , HOH E:990 , HOH E:1421
BINDING SITE FOR RESIDUE PRO E 1600
02
AC6
SOFTWARE
ARG F:42 , ASN F:43 , ASN F:69 , ARG F:105 , HIS F:463 , TYR F:465 , ILE F:468 , PHE F:469 , PRO F:470 , HOH F:1422 , HOH F:1622
BINDING SITE FOR RESIDUE PRO F 1600
03
AC7
SOFTWARE
ARG G:42 , ASN G:43 , ASN G:69 , ARG G:105 , HIS G:463 , TYR G:465 , ILE G:468 , PHE G:469 , PRO G:470 , HOH G:922
BINDING SITE FOR RESIDUE PRO G 1600
04
AC8
SOFTWARE
ARG H:42 , ASN H:43 , ASN H:69 , ARG H:105 , HIS H:463 , TYR H:465 , ILE H:468 , PHE H:469 , PRO H:470
BINDING SITE FOR RESIDUE PRO H 1600
05
FC2
SOFTWARE
GLU E:271 , ASP E:295 , PYR E:1500 , HOH E:1638
BINDING SITE FOR RESIDUE MN E 640
06
FC3
SOFTWARE
LYS E:269 , GLU E:271 , ALA E:292 , ARG E:293 , GLY E:294 , ASP E:295 , THR E:327 , MN E:640 , HOH E:1638
BINDING SITE FOR RESIDUE PYR E 1500
07
FC4
SOFTWARE
ASN E:74 , SER E:76 , ASP E:112 , THR E:113 , HOH E:1051
BINDING SITE FOR RESIDUE K E 1700
08
FC5
SOFTWARE
LYS E:124 , GLY E:125 , SER E:126 , GLY E:127 , THR E:128
BINDING SITE FOR RESIDUE NA E 2000
09
FC6
SOFTWARE
THR E:431 , SER E:433 , SER E:436 , HOH E:1310 , HOH E:1396
BINDING SITE FOR RESIDUE NA E 2100
10
FC7
SOFTWARE
PRO E:38
BINDING SITE FOR RESIDUE EDO E 6015
11
FC8
SOFTWARE
ASP E:177 , GLY E:294 , HOH E:565
BINDING SITE FOR RESIDUE EDO E 6039
12
FC9
SOFTWARE
ILE E:50 , GLY E:51 , PRO E:52 , ASN E:74 , ALA E:365 , HOH E:1198
BINDING SITE FOR RESIDUE EDO E 6046
13
GC1
SOFTWARE
ARG E:254 , GLU E:284 , ALA E:285 , ASP E:287 , LYS E:321
BINDING SITE FOR RESIDUE EDO E 6049
14
GC2
SOFTWARE
PRO E:116 , ASN E:209 , LEU E:210 , VAL E:215 , ARG E:245 , GLU E:299
BINDING SITE FOR RESIDUE GOL E 6205
15
GC3
SOFTWARE
GLU E:117 , ILE E:118 , VAL E:208 , PHE E:243 , ASP E:295
BINDING SITE FOR RESIDUE GOL E 6305
16
GC4
SOFTWARE
GLU F:271 , ASP F:295 , HOH F:1199 , PYR F:1500 , HOH F:1624
BINDING SITE FOR RESIDUE MN F 640
17
GC5
SOFTWARE
LYS F:269 , GLU F:271 , ALA F:292 , ARG F:293 , GLY F:294 , ASP F:295 , THR F:327 , MN F:640 , HOH F:668 , HOH F:1199
BINDING SITE FOR RESIDUE PYR F 1500
18
GC6
SOFTWARE
ASN F:74 , SER F:76 , ASP F:112 , THR F:113 , SER F:242 , HOH F:1656
BINDING SITE FOR RESIDUE K F 1700
19
GC7
SOFTWARE
THR F:431 , SER F:433 , SER F:436 , HOH F:1339
BINDING SITE FOR RESIDUE NA F 2000
20
GC8
SOFTWARE
ASP F:177 , GLN F:328 , HOH F:572 , HOH F:744 , ARG H:338 , PRO H:339 , THR H:340 , ARG H:341
BINDING SITE FOR RESIDUE GOL F 6010
21
GC9
SOFTWARE
ALA F:37 , PRO F:38 , THR F:40 , ARG F:382
BINDING SITE FOR RESIDUE EDO F 6012
22
HC1
SOFTWARE
PRO F:116 , VAL F:208 , ASN F:209 , LEU F:210 , VAL F:215 , PHE F:243 , ARG F:245 , GLU F:299
BINDING SITE FOR RESIDUE GOL F 6206
23
HC2
SOFTWARE
GLU F:117 , ILE F:118 , GLY F:207 , VAL F:208 , PHE F:243 , ASP F:295 , HOH F:1624
BINDING SITE FOR RESIDUE GOL F 6306
24
HC3
SOFTWARE
GLU G:271 , ASP G:295 , HOH G:1201 , HOH G:1408 , PYR G:1500
BINDING SITE FOR RESIDUE MN G 640
25
HC4
SOFTWARE
LYS G:269 , GLU G:271 , ALA G:292 , ARG G:293 , GLY G:294 , ASP G:295 , THR G:327 , MN G:640 , HOH G:651 , HOH G:1408
BINDING SITE FOR RESIDUE PYR G 1500
26
HC5
SOFTWARE
ASN G:74 , SER G:76 , ASP G:112 , THR G:113 , SER G:242 , HOH G:651 , HOH G:1409
BINDING SITE FOR RESIDUE K G 1700
27
HC6
SOFTWARE
THR G:431 , SER G:436
BINDING SITE FOR RESIDUE NA G 2000
28
HC7
SOFTWARE
PRO G:116 , ASN G:209 , LEU G:210 , VAL G:215 , PHE G:243 , ARG G:245 , GLU G:299 , GOL G:6307
BINDING SITE FOR RESIDUE GOL G 6207
29
HC8
SOFTWARE
GLU G:117 , ILE G:118 , GLY G:207 , VAL G:208 , PHE G:243 , ASP G:295 , HOH G:1201 , GOL G:6207
BINDING SITE FOR RESIDUE GOL G 6307
30
HC9
SOFTWARE
GLU H:271 , ASP H:295 , HOH H:1202 , PYR H:1500 , HOH H:1607
BINDING SITE FOR RESIDUE MN H 640
31
IC1
SOFTWARE
LYS H:269 , GLU H:271 , ALA H:292 , ARG H:293 , GLY H:294 , ASP H:295 , THR H:327 , MN H:640 , HOH H:1202 , HOH H:1607
BINDING SITE FOR RESIDUE PYR H 1500
32
IC2
SOFTWARE
ASN H:74 , SER H:76 , ASP H:112 , THR H:113 , HOH H:1064 , HOH H:1418
BINDING SITE FOR RESIDUE K H 1700
33
IC3
SOFTWARE
LYS H:124 , GLY H:125 , SER H:126 , GLY H:127 , THR H:128
BINDING SITE FOR RESIDUE NA H 2000
34
IC4
SOFTWARE
THR H:431 , SER H:433 , SER H:436 , HOH H:1397
BINDING SITE FOR RESIDUE NA H 2100
35
IC5
SOFTWARE
GLU H:284 , ALA H:285 , SER H:286 , ASP H:287 , LYS H:321
BINDING SITE FOR RESIDUE EDO H 6037
36
IC6
SOFTWARE
GLU H:117 , ILE H:118 , GLY H:207 , VAL H:208 , PHE H:243 , ASP H:295 , HOH H:1202
BINDING SITE FOR RESIDUE GOL H 6308
[
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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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Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: PYRUVATE_KINASE (E:264-276,F:264-276,G:264-276,H: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
-
-
-
-
E:264-276
F:264-276
G:264-276
H:264-276
[
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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
(0, 0)
Info
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CATH Domains
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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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