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2FV7
Asym. Unit
Info
Asym.Unit (102 KB)
Biol.Unit 1 (95 KB)
Biol.Unit 2 (96 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN RIBOKINASE
Authors
:
W. M. Rabeh, W. Tempel, L. Nedyalkova, C. Arrowsmith, A. Edwards, M. Sun J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium
Date
:
30 Jan 06 (Deposition) - 28 Feb 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (1x)
Keywords
:
Ribokinase, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. M. Rabeh, W. Tempel, L. Nedyalkova, C. Arrowsmith, A. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Crystal Structure Of Human Ribokinase
To Be Published
[
close entry info
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Hetero Components
(4, 18)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
4a: UNKNOWN ATOM OR ION (UNXa)
4b: UNKNOWN ATOM OR ION (UNXb)
4c: UNKNOWN ATOM OR ION (UNXc)
4d: UNKNOWN ATOM OR ION (UNXd)
4e: UNKNOWN ATOM OR ION (UNXe)
4f: UNKNOWN ATOM OR ION (UNXf)
4g: UNKNOWN ATOM OR ION (UNXg)
4h: UNKNOWN ATOM OR ION (UNXh)
4i: UNKNOWN ATOM OR ION (UNXi)
4j: UNKNOWN ATOM OR ION (UNXj)
4k: UNKNOWN ATOM OR ION (UNXk)
4l: UNKNOWN ATOM OR ION (UNXl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
2
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
MG
2
Ligand/Ion
MAGNESIUM ION
3
NA
2
Ligand/Ion
SODIUM ION
4
UNX
12
Ligand/Ion
UNKNOWN ATOM OR ION
[
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Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:263 , SER A:301 , ALA A:304 , SER A:310 , HOH A:878 , HOH A:879
BINDING SITE FOR RESIDUE NA A 403
02
AC2
SOFTWARE
ADP A:401 , HOH A:817 , HOH A:819 , HOH A:825
BINDING SITE FOR RESIDUE MG A 404
03
AC3
SOFTWARE
ASP B:263 , SER B:301 , ALA B:304 , SER B:310 , HOH B:845 , HOH B:853
BINDING SITE FOR RESIDUE NA B 405
04
AC4
SOFTWARE
ADP B:402 , HOH B:842 , HOH B:859 , HOH B:864 , HOH B:871
BINDING SITE FOR RESIDUE MG B 406
05
AC5
SOFTWARE
ASN A:199 , THR A:235 , LEU A:236 , GLY A:237 , GLY A:240 , THR A:256 , GLU A:257 , VAL A:259 , ALA A:267 , GLY A:268 , ASN A:295 , ALA A:298 , VAL A:302 , MG A:404 , HOH A:805 , HOH A:856
BINDING SITE FOR RESIDUE ADP A 401
06
AC6
SOFTWARE
ASN B:199 , THR B:235 , LEU B:236 , GLY B:237 , ALA B:238 , GLY B:240 , THR B:256 , GLU B:257 , VAL B:259 , GLY B:268 , ASN B:295 , ALA B:298 , MG B:406 , HOH B:871
BINDING SITE FOR RESIDUE ADP B 402
07
AC7
SOFTWARE
VAL A:21 , GLY A:22 , CYS A:151 , GLN A:152 , ILE A:155 , SER A:160 , HOH A:801
BINDING SITE FOR RESIDUE UNX A 501
08
AC8
SOFTWARE
VAL B:21 , GLN B:152 , ILE B:155 , SER B:160 , HOH B:807
BINDING SITE FOR RESIDUE UNX B 502
09
AC9
SOFTWARE
GLY B:53 , ASN B:57
BINDING SITE FOR RESIDUE UNX B 503
10
BC1
SOFTWARE
LYS B:173
BINDING SITE FOR RESIDUE UNX B 504
11
BC2
SOFTWARE
ASP B:78
BINDING SITE FOR RESIDUE UNX B 505
12
BC3
SOFTWARE
LYS A:173 , ASP A:194
BINDING SITE FOR RESIDUE UNX A 506
13
BC4
SOFTWARE
GLY A:171 , LYS B:46
BINDING SITE FOR RESIDUE UNX A 507
14
BC5
SOFTWARE
LYS A:54 , ASP A:269 , HOH A:856
BINDING SITE FOR RESIDUE UNX A 510
15
BC6
SOFTWARE
PHE B:51
BINDING SITE FOR RESIDUE UNX B 511
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PFKB_KINASES_2 (A:263-276,B:263-276)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PFKB_KINASES_2
PS00584
pfkB family of carbohydrate kinases signature 2.
RBSK_HUMAN
263-276
2
A:263-276
B:263-276
[
close PROSITE info
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Exons
(8, 16)
Info
All Exons
Exon 1.1a (A:15-30 | B:15-30)
Exon 1.4b (A:30-74 | B:30-74)
Exon 1.5 (A:75-96 | B:75-96)
Exon 1.6 (A:96-117 | B:96-117)
Exon 1.7a (A:117-172 | B:117-172)
Exon 1.8 (A:172-202 | B:172-202)
Exon 1.9 (A:203-265 | B:203-265)
Exon 1.11b (A:266-322 | B:266-322)
View:
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All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.4b
3: Boundary 1.4b/1.5
4: Boundary 1.5/1.6
5: Boundary 1.6/1.7a
6: Boundary 1.7a/1.8
7: Boundary 1.8/1.9
8: Boundary 1.9/1.11b
9: Boundary 1.11b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000302188
1a
ENSE00001260860
chr2:
28113965-28113124
842
RBSK_HUMAN
1-30
30
2
A:15-30
B:15-30
16
16
1.4b
ENST00000302188
4b
ENSE00001709591
chr2:
28081438-28081306
133
RBSK_HUMAN
30-74
45
2
A:30-74
B:30-74
45
45
1.5
ENST00000302188
5
ENSE00001794033
chr2:
28070964-28070901
64
RBSK_HUMAN
75-96
22
2
A:75-96
B:75-96
22
22
1.6
ENST00000302188
6
ENSE00001785669
chr2:
28069971-28069909
63
RBSK_HUMAN
96-117
22
2
A:96-117
B:96-117
22
22
1.7a
ENST00000302188
7a
ENSE00001600483
chr2:
28066098-28065934
165
RBSK_HUMAN
117-172
56
2
A:117-172
B:117-172
56
56
1.8
ENST00000302188
8
ENSE00001652758
chr2:
28055644-28055553
92
RBSK_HUMAN
172-202
31
2
A:172-202
B:172-202
31
31
1.9
ENST00000302188
9
ENSE00001766843
chr2:
28050622-28050434
189
RBSK_HUMAN
203-265
63
2
A:203-265
B:203-265
63
63
1.11b
ENST00000302188
11b
ENSE00001260853
chr2:
28004655-28004231
425
RBSK_HUMAN
266-322
57
2
A:266-322
B:266-322
57
57
[
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]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2fv7a1 (A:15-322)
1b: SCOP_d2fv7b_ (B:)
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Folds
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribokinase-like
(226)
Superfamily
:
Ribokinase-like
(189)
Family
:
Ribokinase-like
(36)
Protein domain
:
Ribokinase
(7)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d2fv7a1
A:15-322
1b
d2fv7b_
B:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2fv7A00 (A:15-322)
1b: CATH_2fv7B00 (B:15-322)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
(109)
Homologous Superfamily
:
[code=3.40.1190.20, no name defined]
(73)
Human (Homo sapiens)
(10)
1a
2fv7A00
A:15-322
1b
2fv7B00
B:15-322
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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Atom Selection
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Protein
Nucleic
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Protein & NOT Site
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Asymmetric Unit 1
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