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1NKH
Asym. Unit
Info
Asym.Unit (153 KB)
Biol.Unit 1 (76 KB)
Biol.Unit 2 (75 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF LACTOSE SYNTHASE COMPLEX WITH UDP AND MANGANESE
Authors
:
B. Ramakrishnan, P. K. Qasba
Date
:
03 Jan 03 (Deposition) - 14 Jan 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Lactose Synthease, Udp And Mn Binding, Transferase Activator/Transferase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Ramakrishnan, P. K. Qasba
Crystal Structure Of Lactose Synthase Reveals A Large Conformational Change In Its Catalytic Component, The Beta-1, 4-Galactosyltransferase
J. Mol. Biol. V. 310 205 2001
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 15)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
3a: TETRAETHYLENE GLYCOL (PG4a)
3b: TETRAETHYLENE GLYCOL (PG4b)
3c: TETRAETHYLENE GLYCOL (PG4c)
3d: TETRAETHYLENE GLYCOL (PG4d)
3e: TETRAETHYLENE GLYCOL (PG4e)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
5a: URIDINE-5'-DIPHOSPHATE (UDPa)
5b: URIDINE-5'-DIPHOSPHATE (UDPb)
5c: URIDINE-5'-DIPHOSPHATE (UDPc)
5d: URIDINE-5'-DIPHOSPHATE (UDPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
MN
2
Ligand/Ion
MANGANESE (II) ION
3
PG4
5
Ligand/Ion
TETRAETHYLENE GLYCOL
4
SO4
2
Ligand/Ion
SULFATE ION
5
UDP
4
Ligand/Ion
URIDINE-5'-DIPHOSPHATE
[
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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:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:79 , ASP A:82 , GLU A:84 , ASP A:87 , ASP A:88 , HOH A:909 , HOH A:945
BINDING SITE FOR RESIDUE CA A 805
02
AC2
SOFTWARE
LYS C:79 , ASP C:82 , GLU C:84 , ASP C:87 , ASP C:88 , HOH C:910 , HOH C:922
BINDING SITE FOR RESIDUE CA C 806
03
AC3
SOFTWARE
ASP B:254 , MET B:344 , HIS B:347 , UDP B:809 , HOH B:908
BINDING SITE FOR RESIDUE MN B 807
04
AC4
SOFTWARE
ASP D:254 , MET D:344 , HIS D:347 , UDP D:810 , HOH D:902
BINDING SITE FOR RESIDUE MN D 808
05
AC5
SOFTWARE
GLU D:148 , PHE D:149 , ASN D:150 , ARG D:343
BINDING SITE FOR RESIDUE SO4 D 818
06
AC6
SOFTWARE
THR A:4 , LYS A:7 , HOH A:1077 , HOH A:1288
BINDING SITE FOR RESIDUE SO4 A 819
07
AC7
SOFTWARE
PRO B:187 , PHE B:188 , ARG B:189 , ARG B:191 , PHE B:226 , ASP B:252 , VAL B:253 , ASP B:254 , TRP B:314 , MET B:344 , HIS B:347 , ASP B:350 , MN B:807 , PG4 B:817 , HOH B:908 , HOH B:912 , HOH B:937 , HOH B:959 , HOH B:976 , HOH B:992 , HOH B:1026 , HOH B:1210
BINDING SITE FOR RESIDUE UDP B 809
08
AC8
SOFTWARE
PRO D:187 , PHE D:188 , ARG D:189 , ARG D:191 , PHE D:226 , ASP D:252 , VAL D:253 , ASP D:254 , TRP D:314 , MET D:344 , HIS D:347 , ARG D:349 , ASP D:350 , MN D:808 , PG4 D:816 , HOH D:902 , HOH D:919 , HOH D:925 , HOH D:931 , HOH D:1018 , HOH D:1181
BINDING SITE FOR RESIDUE UDP D 810
09
AC9
SOFTWARE
LEU B:155 , LYS B:156 , GLU B:159 , GLN B:192 , GLN B:386 , TYR B:388 , PRO B:389 , LEU B:390 , TYR B:391 , LYS B:393
BINDING SITE FOR RESIDUE UDP B 811
10
BC1
SOFTWARE
LEU D:155 , LYS D:156 , GLU D:159 , GLN D:386 , TYR D:388 , PRO D:389 , LEU D:390 , TYR D:391 , HOH D:958 , HOH D:1285 , HOH D:1301 , HOH D:1331
BINDING SITE FOR RESIDUE UDP D 812
11
BC2
SOFTWARE
GLU A:2 , PHE A:31 , HIS A:32 , SER A:34 , GLY A:35 , ALA A:40 , HOH A:940 , HOH A:1279 , LYS B:279 , TRP B:314 , ARG B:349 , PG4 B:817
BINDING SITE FOR RESIDUE PG4 A 813
12
BC3
SOFTWARE
PHE C:31 , HIS C:32 , THR C:33 , SER C:34 , GLY C:35 , ASP C:37 , ALA C:40 , HOH C:967 , HOH C:1183 , TRP D:314 , ARG D:359 , PG4 D:816
BINDING SITE FOR RESIDUE PG4 C 814
13
BC4
SOFTWARE
ASP B:242 , VAL B:385 , ARG B:387 , HOH B:1107 , HOH B:1287 , HOH B:1495 , ARG D:387
BINDING SITE FOR RESIDUE PG4 B 815
14
BC5
SOFTWARE
PHE C:31 , PG4 C:814 , LYS D:279 , PHE D:280 , TYR D:286 , TYR D:289 , GLY D:292 , TRP D:314 , ASP D:318 , UDP D:810 , HOH D:1132 , HOH D:1159 , HOH D:1181 , HOH D:1281
BINDING SITE FOR RESIDUE PG4 D 816
15
BC6
SOFTWARE
PHE A:31 , PG4 A:813 , LYS B:279 , PHE B:280 , TYR B:286 , TRP B:314 , GLY B:316 , ASP B:318 , ASP B:319 , UDP B:809 , HOH B:912 , HOH B:1026 , HOH B:1190 , HOH B:1240
BINDING SITE FOR RESIDUE PG4 B 817
[
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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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: LACTALBUMIN_LYSOZYME_2 (A:1-123,C:1-123)
2: LACTALBUMIN_LYSOZYME_1 (A:73-91,C:73-91)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LACTALBUMIN_LYSOZYME_2
PS51348
Alpha-lactalbumin / lysozyme C family profile.
LALBA_MOUSE
21-143
2
A:1-123
C:1-123
2
LACTALBUMIN_LYSOZYME_1
PS00128
Alpha-lactalbumin / lysozyme C signature.
LALBA_MOUSE
93-111
2
A:73-91
C:73-91
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]
Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1nkha_ (A:)
1b: SCOP_d1nkhc_ (C:)
2a: SCOP_d1nkhb_ (B:)
2b: SCOP_d1nkhd_ (D:)
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Superfamilies
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)
(
)
Families
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Lysozyme-like
(1361)
Superfamily
:
Lysozyme-like
(1361)
Family
:
C-type lysozyme
(738)
Protein domain
:
alpha-Lactalbumin
(25)
Mouse (Mus musculus) [TaxId: 10090]
(12)
1a
d1nkha_
A:
1b
d1nkhc_
C:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleotide-diphospho-sugar transferases
(408)
Superfamily
:
Nucleotide-diphospho-sugar transferases
(408)
Family
:
beta 1,4 galactosyltransferase (b4GalT1)
(39)
Protein domain
:
beta 1,4 galactosyltransferase (b4GalT1)
(20)
Cow (Bos taurus) [TaxId: 9913]
(20)
2a
d1nkhb_
B:
2b
d1nkhd_
D:
[
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]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1nkhB00 (B:131-402)
1b: CATH_1nkhD00 (D:131-402)
2a: CATH_1nkhA00 (A:1-123)
2b: CATH_1nkhC00 (C:1-123)
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Topologies
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
Homologous Superfamily
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
House mouse (Mus musculus)
(18)
1a
1nkhB00
B:131-402
1b
1nkhD00
D:131-402
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Lysozyme
(1131)
Homologous Superfamily
:
[code=1.10.530.10, no name defined]
(605)
House mouse (Mus musculus)
(61)
2a
1nkhA00
A:1-123
2b
1nkhC00
C:1-123
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Glyco_transf_7C_1nkhD01 (D:271-350)
1b: PFAM_Glyco_transf_7C_1nkhD02 (D:271-350)
2a: PFAM_Glyco_transf_7N_1nkhD03 (D:134-269)
2b: PFAM_Glyco_transf_7N_1nkhD04 (D:134-269)
3a: PFAM_Lys_1nkhC01 (C:1-120)
3b: PFAM_Lys_1nkhC02 (C:1-120)
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Clans
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)
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Organisms
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)
(
)
Clan
:
GT-A
(172)
Family
:
Glyco_transf_7C
(16)
Bos taurus (Bovine)
(15)
1a
Glyco_transf_7C-1nkhD01
D:271-350
1b
Glyco_transf_7C-1nkhD02
D:271-350
Family
:
Glyco_transf_7N
(16)
Bos taurus (Bovine)
(15)
2a
Glyco_transf_7N-1nkhD03
D:134-269
2b
Glyco_transf_7N-1nkhD04
D:134-269
Clan
:
Lysozyme
(266)
Family
:
Lys
(245)
Mus musculus (Mouse)
(10)
3a
Lys-1nkhC01
C:1-120
3b
Lys-1nkhC02
C:1-120
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Asym.Unit (153 KB)
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