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1NKH
Biol. Unit 1
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
(3, 6)
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
-1
Ligand/Ion
CALCIUM ION
2
MN
-1
Ligand/Ion
MANGANESE (II) ION
3
PG4
3
Ligand/Ion
TETRAETHYLENE GLYCOL
4
SO4
1
Ligand/Ion
SULFATE ION
5
UDP
2
Ligand/Ion
URIDINE-5'-DIPHOSPHATE
[
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]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC6 (SOFTWARE)
4: AC7 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC2 (SOFTWARE)
7: BC4 (SOFTWARE)
8: BC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
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
2
AC3
SOFTWARE
ASP B:254 , MET B:344 , HIS B:347 , UDP B:809 , HOH B:908
BINDING SITE FOR RESIDUE MN B 807
3
AC6
SOFTWARE
THR A:4 , LYS A:7 , HOH A:1077 , HOH A:1288
BINDING SITE FOR RESIDUE SO4 A 819
4
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
5
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
6
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
7
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
8
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 only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: LACTALBUMIN_LYSOZYME_2 (A:1-123)
2: LACTALBUMIN_LYSOZYME_1 (A: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
1
A:1-123
-
2
LACTALBUMIN_LYSOZYME_1
PS00128
Alpha-lactalbumin / lysozyme C signature.
LALBA_MOUSE
93-111
1
A: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.
(no "Exon" information available for biological units yet)
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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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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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(
)
(
)
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
[
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]
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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)
(
)
Families
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)
(
)
Organisms
(
)
(
)
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)
Header - Asym.Unit
Biol.Unit 1 (76 KB)
Header - Biol.Unit 1
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