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4IP7
Asym. Unit
Info
Asym.Unit (699 KB)
Biol.Unit 1 (685 KB)
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(1)
Title
:
STRUCTURE OF THE S12D VARIANT OF HUMAN LIVER PYRUVATE KINASE IN COMPLEX WITH CITRATE AND FBP.
Authors
:
T. Holyoak, A. W. Fenton
Date
:
09 Jan 13 (Deposition) - 30 Jan 13 (Release) - 06 Feb 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Kinase, Glycolysis, Allosteric, Phosphorylation Mimic, Liver, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Holyoak, B. Zhang, J. Deng, Q. Tang, C. B. Prasannan, A. W. Fenton
Energetic Coupling Between An Oxidizable Cysteine And The Phosphorylatable N-Terminus Of Human Liver Pyruvate Kinase.
Biochemistry V. 52 466 2013
[
close entry info
]
Hetero Components
(8, 30)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
2a: ADENOSINE (ADNa)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
4a: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPa)
4b: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPb)
4c: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPc)
4d: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPd)
5a: CITRATE ANION (FLCa)
5b: CITRATE ANION (FLCb)
5c: CITRATE ANION (FLCc)
5d: CITRATE ANION (FLCd)
6a: MANGANESE (II) ION (MNa)
6b: MANGANESE (II) ION (MNb)
6c: MANGANESE (II) ION (MNc)
6d: MANGANESE (II) ION (MNd)
7a: SODIUM ION (NAa)
7b: SODIUM ION (NAb)
7c: SODIUM ION (NAc)
7d: SODIUM ION (NAd)
8a: DI(HYDROXYETHYL)ETHER (PEGa)
8b: DI(HYDROXYETHYL)ETHER (PEGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
2
Ligand/Ion
PENTAETHYLENE GLYCOL
2
ADN
1
Ligand/Ion
ADENOSINE
3
EDO
9
Ligand/Ion
1,2-ETHANEDIOL
4
FBP
4
Ligand/Ion
BETA-FRUCTOSE-1,6-DIPHOSPHATE
5
FLC
4
Ligand/Ion
CITRATE ANION
6
MN
4
Ligand/Ion
MANGANESE (II) ION
7
NA
4
Ligand/Ion
SODIUM ION
8
PEG
2
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
close Hetero Component info
]
Sites
(30, 30)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:284 , ASP A:308 , FLC A:602 , HOH A:721 , HOH A:1006
BINDING SITE FOR RESIDUE MN A 601
02
AC2
SOFTWARE
ARG A:85 , ASP A:125 , LYS A:282 , GLU A:284 , MET A:303 , ALA A:305 , ARG A:306 , GLY A:307 , ASP A:308 , THR A:340 , MET A:372 , MN A:601 , NA A:607 , HOH A:721 , HOH A:729 , HOH A:781 , HOH A:912 , HOH A:1005 , HOH A:1006
BINDING SITE FOR RESIDUE FLC A 602
03
AC3
SOFTWARE
LEU A:443 , THR A:444 , THR A:445 , THR A:446 , SER A:449 , TRP A:494 , ARG A:501 , GLY A:526 , ARG A:528 , PRO A:529 , GLY A:530 , SER A:531 , GLY A:532 , TYR A:533 , THR A:534 , HOH A:705 , HOH A:707 , HOH A:719 , HOH A:728 , HOH A:759 , HOH A:764 , HOH A:770 , HOH A:784 , HOH A:933
BINDING SITE FOR RESIDUE FBP A 603
04
AC4
SOFTWARE
GLY A:333 , LYS A:334 , PRO A:335 , ASP A:369 , GLN A:451 , SER A:454 , ARG A:455 , ARG A:457 , CYS A:478 , HOH A:730
BINDING SITE FOR RESIDUE EDO A 604
05
AC5
SOFTWARE
LYS A:278 , GLN A:451 , GLN A:474 , HOH A:717 , HOH A:757 , HOH A:762
BINDING SITE FOR RESIDUE EDO A 605
06
AC6
SOFTWARE
ARG A:411 , HIS B:403 , ARG B:404 , PHE B:407 , PHE B:433 , ARG B:459 , HOH B:748 , HOH B:910
BINDING SITE FOR RESIDUE PEG A 606
07
AC7
SOFTWARE
ARG A:85 , ASN A:87 , SER A:89 , ASP A:125 , THR A:126 , FLC A:602 , HOH A:781
BINDING SITE FOR RESIDUE NA A 607
08
AC8
SOFTWARE
GLU B:284 , ASP B:308 , FLC B:602 , HOH B:720 , HOH B:736
BINDING SITE FOR RESIDUE MN B 601
09
AC9
SOFTWARE
ARG B:85 , ASP B:125 , LYS B:282 , GLU B:284 , MET B:303 , ALA B:305 , ARG B:306 , GLY B:307 , ASP B:308 , THR B:340 , MET B:372 , SER B:374 , MN B:601 , NA B:607 , HOH B:720 , HOH B:837 , HOH B:972 , HOH B:1024
BINDING SITE FOR RESIDUE FLC B 602
10
BC1
SOFTWARE
LEU B:443 , THR B:444 , THR B:445 , THR B:446 , SER B:449 , TRP B:494 , ARG B:501 , GLY B:526 , ARG B:528 , PRO B:529 , GLY B:530 , SER B:531 , GLY B:532 , TYR B:533 , THR B:534 , HOH B:710 , HOH B:732 , HOH B:742 , HOH B:745 , HOH B:784 , HOH B:792 , HOH B:797 , HOH B:800 , HOH B:821
BINDING SITE FOR RESIDUE FBP B 603
11
BC2
SOFTWARE
GLY B:333 , LYS B:334 , PRO B:335 , ASP B:369 , GLN B:451 , SER B:454 , ARG B:455 , ARG B:457 , CYS B:478 , HOH B:714
BINDING SITE FOR RESIDUE EDO B 604
12
BC3
SOFTWARE
HIS B:93 , HOH B:750 , HOH B:947 , EDO C:607
BINDING SITE FOR RESIDUE PEG B 605
13
BC4
SOFTWARE
SER B:56 , THR B:57 , SER B:58 , HIS B:476 , VAL B:481 , PHE B:482 , HOH B:739 , HOH B:971 , HOH B:1014
BINDING SITE FOR RESIDUE EDO B 606
14
BC5
SOFTWARE
ARG B:85 , ASN B:87 , SER B:89 , ASP B:125 , THR B:126 , LYS B:282 , FLC B:602 , HOH B:1024
BINDING SITE FOR RESIDUE NA B 607
15
BC6
SOFTWARE
ASP A:190 , GLN A:341 , ARG C:351 , PRO C:352 , ARG C:354 , HOH C:966
BINDING SITE FOR RESIDUE EDO C 601
16
BC7
SOFTWARE
GLU C:284 , ASP C:308 , FLC C:603 , HOH C:716 , HOH C:752
BINDING SITE FOR RESIDUE MN C 602
17
BC8
SOFTWARE
ARG C:85 , ASP C:125 , LYS C:282 , GLU C:284 , MET C:303 , ALA C:305 , ARG C:306 , GLY C:307 , ASP C:308 , THR C:340 , MET C:372 , SER C:374 , MN C:602 , NA C:608 , HOH C:716 , HOH C:752 , HOH C:815 , HOH C:837
BINDING SITE FOR RESIDUE FLC C 603
18
BC9
SOFTWARE
LEU C:443 , THR C:444 , THR C:445 , THR C:446 , SER C:449 , TRP C:494 , ARG C:501 , GLY C:526 , ARG C:528 , PRO C:529 , GLY C:530 , SER C:531 , GLY C:532 , TYR C:533 , THR C:534 , HOH C:708 , HOH C:713 , HOH C:722 , HOH C:828 , HOH C:855 , HOH C:861 , HOH C:864 , HOH C:883 , HOH C:983
BINDING SITE FOR RESIDUE FBP C 604
19
CC1
SOFTWARE
GLY C:91
BINDING SITE FOR RESIDUE 1PE C 605
20
CC2
SOFTWARE
SER C:56 , THR C:57 , SER C:58 , ASN C:82 , ASP C:369 , HIS C:476 , LEU C:477 , CYS C:478 , ARG C:479 , GLY C:480 , VAL C:481 , PHE C:482 , HOH C:734 , HOH C:881
BINDING SITE FOR RESIDUE 1PE C 606
21
CC3
SOFTWARE
PEG B:605 , HIS C:93
BINDING SITE FOR RESIDUE EDO C 607
22
CC4
SOFTWARE
ARG C:85 , ASN C:87 , SER C:89 , ASP C:125 , THR C:126 , FLC C:603 , HOH C:1033
BINDING SITE FOR RESIDUE NA C 608
23
CC5
SOFTWARE
GLU D:284 , ASP D:308 , FLC D:602 , HOH D:703 , HOH D:751
BINDING SITE FOR RESIDUE MN D 601
24
CC6
SOFTWARE
ARG D:85 , ASP D:125 , LYS D:282 , GLU D:284 , MET D:303 , ALA D:305 , ARG D:306 , GLY D:307 , ASP D:308 , THR D:340 , MET D:372 , MN D:601 , NA D:608 , HOH D:703 , HOH D:738 , HOH D:741 , HOH D:751
BINDING SITE FOR RESIDUE FLC D 602
25
CC7
SOFTWARE
LEU D:443 , THR D:444 , THR D:445 , THR D:446 , SER D:449 , TRP D:494 , ARG D:501 , GLY D:526 , ARG D:528 , PRO D:529 , GLY D:530 , SER D:531 , GLY D:532 , TYR D:533 , THR D:534 , HOH D:705 , HOH D:709 , HOH D:723 , HOH D:767 , HOH D:769 , HOH D:777 , HOH D:807 , HOH D:826 , HOH D:889
BINDING SITE FOR RESIDUE FBP D 603
26
CC8
SOFTWARE
ARG D:68 , GLU D:98 , ASN D:102 , HOH D:756
BINDING SITE FOR RESIDUE ADN D 604
27
CC9
SOFTWARE
GLY D:333 , LYS D:334 , PRO D:335 , ASP D:369 , GLN D:451 , SER D:454 , ARG D:455 , ARG D:457 , CYS D:478 , HOH D:808
BINDING SITE FOR RESIDUE EDO D 605
28
DC1
SOFTWARE
ARG D:267 , GLU D:297 , SER D:299 , ASP D:300 , LYS D:334
BINDING SITE FOR RESIDUE EDO D 606
29
DC2
SOFTWARE
LYS D:278 , GLN D:451 , GLN D:474 , HOH D:728 , HOH D:783 , HOH D:799
BINDING SITE FOR RESIDUE EDO D 607
30
DC3
SOFTWARE
ARG D:85 , ASN D:87 , SER D:89 , ASP D:125 , THR D:126 , FLC D:602 , HOH D:738 , HOH D:1005
BINDING SITE FOR RESIDUE NA D 608
[
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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
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
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CATH Domains
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Pfam Domains
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Sorry, no Info available
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