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1YJX
Asym. Unit
Info
Asym.Unit (474 KB)
Biol.Unit 1 (85 KB)
Biol.Unit 2 (83 KB)
Biol.Unit 3 (82 KB)
Biol.Unit 4 (81 KB)
Biol.Unit 5 (83 KB)
Biol.Unit 6 (83 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN B TYPE PHOSPHOGLYCERATE MUTASE
Authors
:
Y. Wang, Z. Wei, L. Liu, W. Gong
Date
:
16 Jan 05 (Deposition) - 17 May 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Biol. Unit 5: I,J (1x)
Biol. Unit 6: K,L (1x)
Keywords
:
Alpha/Beta, Isomerase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Wang, Z. Wei, L. Liu, Z. Cheng, Y. Lin, F. Ji, W. Gong
Crystal Structure Of Human B-Type Phosphoglycerate Mutase Bound With Citrate.
Biochem. Biophys. Res. Commun. V. 331 1207 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 18)
Info
All Hetero Components
1a: CITRIC ACID (CITa)
1b: CITRIC ACID (CITb)
1c: CITRIC ACID (CITc)
1d: CITRIC ACID (CITd)
1e: CITRIC ACID (CITe)
1f: CITRIC ACID (CITf)
1g: CITRIC ACID (CITg)
1h: CITRIC ACID (CITh)
1i: CITRIC ACID (CITi)
1j: CITRIC ACID (CITj)
1k: CITRIC ACID (CITk)
1l: CITRIC ACID (CITl)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CIT
12
Ligand/Ion
CITRIC ACID
2
CL
6
Ligand/Ion
CHLORIDE ION
[
close Hetero Component info
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Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:68 , ARG A:83 , TRP B:68 , ARG B:83
BINDING SITE FOR RESIDUE CL A 263
02
AC2
SOFTWARE
TRP C:68 , ARG C:83 , TRP D:68 , ARG D:83
BINDING SITE FOR RESIDUE CL C 263
03
AC3
SOFTWARE
TRP E:68 , ARG E:83 , TRP F:68 , ARG F:83
BINDING SITE FOR RESIDUE CL F 263
04
AC4
SOFTWARE
TRP G:68 , ARG G:83 , TRP H:68 , ARG H:83
BINDING SITE FOR RESIDUE CL H 263
05
AC5
SOFTWARE
TRP I:68 , VAL I:81 , ARG I:83 , TRP J:68 , VAL J:81 , ARG J:83
BINDING SITE FOR RESIDUE CL J 263
06
AC6
SOFTWARE
TRP K:68 , VAL K:81 , ARG K:83 , TRP L:68 , VAL L:81 , ARG L:83
BINDING SITE FOR RESIDUE CL K 263
07
AC7
SOFTWARE
ASN A:17 , SER A:23 , GLY A:24 , TYR A:92 , LYS A:100 , ARG A:116 , HOH A:608 , HOH A:616
BINDING SITE FOR RESIDUE CIT A 601
08
AC8
SOFTWARE
ASN B:17 , SER B:23 , GLY B:24 , GLU B:89 , TYR B:92 , LYS B:100 , HOH B:605 , HOH B:628
BINDING SITE FOR RESIDUE CIT B 602
09
AC9
SOFTWARE
PHE C:22 , SER C:23 , GLY C:24 , GLU C:89 , TYR C:92 , LYS C:100 , ARG C:116 , HOH C:619
BINDING SITE FOR RESIDUE CIT C 603
10
BC1
SOFTWARE
ASN D:17 , SER D:23 , GLY D:24 , GLU D:89 , TYR D:92 , LYS D:100 , ARG D:116 , HOH D:628
BINDING SITE FOR RESIDUE CIT D 604
11
BC2
SOFTWARE
ASN E:17 , SER E:23 , GLY E:24 , GLU E:89 , TYR E:92 , LYS E:100 , ARG E:116
BINDING SITE FOR RESIDUE CIT E 605
12
BC3
SOFTWARE
ARG F:10 , PHE F:22 , SER F:23 , GLY F:24 , GLU F:89 , TYR F:92 , LYS F:100
BINDING SITE FOR RESIDUE CIT F 606
13
BC4
SOFTWARE
ARG G:10 , SER G:23 , GLY G:24 , TYR G:92 , LYS G:100
BINDING SITE FOR RESIDUE CIT G 607
14
BC5
SOFTWARE
ASN H:17 , SER H:23 , GLY H:24 , ARG H:62 , GLU H:89 , TYR H:92 , LYS H:100
BINDING SITE FOR RESIDUE CIT H 608
15
BC6
SOFTWARE
ARG I:10 , PHE I:22 , SER I:23 , GLY I:24 , GLU I:89 , TYR I:92 , LYS I:100 , HOH I:619 , HOH I:621
BINDING SITE FOR RESIDUE CIT I 609
16
BC7
SOFTWARE
PHE J:22 , SER J:23 , GLY J:24 , TYR J:92 , LYS J:100 , ARG J:116
BINDING SITE FOR RESIDUE CIT J 610
17
BC8
SOFTWARE
ARG K:10 , PHE K:22 , SER K:23 , GLY K:24 , GLU K:89 , TYR K:92 , LYS K:100 , ARG K:116
BINDING SITE FOR RESIDUE CIT K 611
18
BC9
SOFTWARE
ARG L:10 , ASN L:17 , SER L:23 , GLY L:24 , TYR L:92 , LYS L:100 , ARG L:116 , HOH L:628
BINDING SITE FOR RESIDUE CIT L 612
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(1, 12)
Info
All PROSITE Patterns/Profiles
1: PG_MUTASE (A:8-17,B:8-17,C:8-17,D:8-17,E:8-17...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PG_MUTASE
PS00175
Phosphoglycerate mutase family phosphohistidine signature.
PGAM1_HUMAN
8-17
12
A:8-17
B:8-17
C:8-17
D:8-17
E:8-17
F:8-17
G:8-17
H:8-17
I:8-17
J:8-17
K:8-17
L:8-17
[
close PROSITE info
]
Exons
(4, 48)
Info
All Exons
Exon 1.1a (A:2-47 | B:2-47 | C:3-47 | D:2-47 ...)
Exon 1.4 (A:47-138 | B:47-138 | C:47-138 | D...)
Exon 1.5a (A:139-199 | B:139-199 | C:139-199 ...)
Exon 1.6c (A:199-246 | B:199-243 | C:199-245 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.4
3: Boundary 1.4/1.5a
4: Boundary 1.5a/1.6c
5: Boundary 1.6c/-
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
ENST00000334828
1a
ENSE00001821632
chr10:
99185917-99186203
287
PGAM1_HUMAN
1-47
47
12
A:2-47
B:2-47
C:3-47
D:2-47
E:2-47
F:3-47
G:2-47
H:4-47
I:4-47
J:3-47
K:3-47
L:2-47
46
46
45
46
46
45
46
44
44
45
45
46
1.4
ENST00000334828
4
ENSE00001139094
chr10:
99190136-99190410
275
PGAM1_HUMAN
47-138
92
12
A:47-138
B:47-138
C:47-138
D:47-138
E:47-138
F:47-138
G:47-138
H:47-138
I:47-138
J:47-138
K:47-138
L:47-138
92
92
92
92
92
92
92
92
92
92
92
92
1.5a
ENST00000334828
5a
ENSE00001139086
chr10:
99190712-99190892
181
PGAM1_HUMAN
139-199
61
12
A:139-199
B:139-199
C:139-199
D:139-199
E:139-199
F:139-199
G:139-199
H:139-199
I:139-199
J:139-199
K:139-199
L:139-199
61
61
61
61
61
61
61
61
61
61
61
61
1.6c
ENST00000334828
6c
ENSE00001367378
chr10:
99192112-99193198
1087
PGAM1_HUMAN
199-254
56
12
A:199-246
B:199-243
C:199-245
D:199-246
E:199-244
F:199-244
G:199-246
H:199-244
I:199-245
J:199-246
K:199-241
L:199-246
48
45
47
48
46
46
48
46
47
48
43
48
[
close EXON info
]
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1yjxa_ (A:)
1b: SCOP_d1yjxb_ (B:)
1c: SCOP_d1yjxc_ (C:)
1d: SCOP_d1yjxd_ (D:)
1e: SCOP_d1yjxe_ (E:)
1f: SCOP_d1yjxf_ (F:)
1g: SCOP_d1yjxg_ (G:)
1h: SCOP_d1yjxh_ (H:)
1i: SCOP_d1yjxi_ (I:)
1j: SCOP_d1yjxj_ (J:)
1k: SCOP_d1yjxk_ (K:)
1l: SCOP_d1yjxl_ (L:)
View:
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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
:
Phosphoglycerate mutase-like
(103)
Superfamily
:
Phosphoglycerate mutase-like
(103)
Family
:
Cofactor-dependent phosphoglycerate mutase
(57)
Protein domain
:
automated matches
(41)
Human (Homo sapiens) [TaxId: 9606]
(11)
1a
d1yjxa_
A:
1b
d1yjxb_
B:
1c
d1yjxc_
C:
1d
d1yjxd_
D:
1e
d1yjxe_
E:
1f
d1yjxf_
F:
1g
d1yjxg_
G:
1h
d1yjxh_
H:
1i
d1yjxi_
I:
1j
d1yjxj_
J:
1k
d1yjxk_
K:
1l
d1yjxl_
L:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1yjxK00 (K:3-241)
1b: CATH_1yjxA00 (A:2-246)
1c: CATH_1yjxD00 (D:2-246)
1d: CATH_1yjxG00 (G:2-246)
1e: CATH_1yjxL00 (L:2-246)
1f: CATH_1yjxH00 (H:4-244)
1g: CATH_1yjxB00 (B:2-243)
1h: CATH_1yjxF00 (F:3-244)
1i: CATH_1yjxI00 (I:4-245)
1j: CATH_1yjxC00 (C:3-245)
1k: CATH_1yjxE00 (E:2-244)
1l: CATH_1yjxJ00 (J:3-246)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Phosphoglycerate mutase-like
(91)
Human (Homo sapiens)
(18)
1a
1yjxK00
K:3-241
1b
1yjxA00
A:2-246
1c
1yjxD00
D:2-246
1d
1yjxG00
G:2-246
1e
1yjxL00
L:2-246
1f
1yjxH00
H:4-244
1g
1yjxB00
B:2-243
1h
1yjxF00
F:3-244
1i
1yjxI00
I:4-245
1j
1yjxC00
C:3-245
1k
1yjxE00
E:2-244
1l
1yjxJ00
J:3-246
[
close CATH info
]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_His_Phos_1_1yjxL01 (L:5-193)
1b: PFAM_His_Phos_1_1yjxL02 (L:5-193)
1c: PFAM_His_Phos_1_1yjxL03 (L:5-193)
1d: PFAM_His_Phos_1_1yjxL04 (L:5-193)
1e: PFAM_His_Phos_1_1yjxL05 (L:5-193)
1f: PFAM_His_Phos_1_1yjxL06 (L:5-193)
1g: PFAM_His_Phos_1_1yjxL07 (L:5-193)
1h: PFAM_His_Phos_1_1yjxL08 (L:5-193)
1i: PFAM_His_Phos_1_1yjxL09 (L:5-193)
1j: PFAM_His_Phos_1_1yjxL10 (L:5-193)
1k: PFAM_His_Phos_1_1yjxL11 (L:5-193)
1l: PFAM_His_Phos_1_1yjxL12 (L:5-193)
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Organisms
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)
Clan
:
PGM
(50)
Family
:
His_Phos_1
(31)
Homo sapiens (Human)
(6)
1a
His_Phos_1-1yjxL01
L:5-193
1b
His_Phos_1-1yjxL02
L:5-193
1c
His_Phos_1-1yjxL03
L:5-193
1d
His_Phos_1-1yjxL04
L:5-193
1e
His_Phos_1-1yjxL05
L:5-193
1f
His_Phos_1-1yjxL06
L:5-193
1g
His_Phos_1-1yjxL07
L:5-193
1h
His_Phos_1-1yjxL08
L:5-193
1i
His_Phos_1-1yjxL09
L:5-193
1j
His_Phos_1-1yjxL10
L:5-193
1k
His_Phos_1-1yjxL11
L:5-193
1l
His_Phos_1-1yjxL12
L:5-193
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