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1XDJ
Asym. Unit
Info
Asym.Unit (243 KB)
Biol.Unit 1 (121 KB)
Biol.Unit 2 (119 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF T. MARITIMA COBALAMIN-INDEPENDENT METHIONINE SYNTHASE COMPLEXED WITH ZN2+ AND HOMOCYSTEINE
Authors
:
R. Pejchal, M. L. Ludwig
Date
:
06 Sep 04 (Deposition) - 01 Mar 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Tim Barrel, Homocysteine, Methyltetrahydrofolate, Zinc, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Pejchal, M. L. Ludwig
Cobalamin-Independent Methionine Synthase (Mete): A Face-To-Face Double Barrel That Evolved By Gene Duplication
Plos Biol. V. 3 E31 2005
(for further references see the
PDB file header
)
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Hetero Components
(5, 42)
Info
All Hetero Components
1a: 2-AMINO-4-MERCAPTO-BUTYRIC ACID (HCSa)
1b: 2-AMINO-4-MERCAPTO-BUTYRIC ACID (HCSb)
2a: MESO-ERYTHRITOL (MRYa)
2b: MESO-ERYTHRITOL (MRYb)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
3ab: SELENOMETHIONINE (MSEab)
3ac: SELENOMETHIONINE (MSEac)
3ad: SELENOMETHIONINE (MSEad)
3ae: SELENOMETHIONINE (MSEae)
3af: SELENOMETHIONINE (MSEaf)
3ag: SELENOMETHIONINE (MSEag)
3ah: SELENOMETHIONINE (MSEah)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
3y: SELENOMETHIONINE (MSEy)
3z: SELENOMETHIONINE (MSEz)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HCS
2
Ligand/Ion
2-AMINO-4-MERCAPTO-BUTYRIC ACID
2
MRY
2
Ligand/Ion
MESO-ERYTHRITOL
3
MSE
34
Mod. Amino Acid
SELENOMETHIONINE
4
SO4
2
Ligand/Ion
SULFATE ION
5
ZN
2
Ligand/Ion
ZINC ION
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG B:85 , TYR B:388 , ARG B:391 , GLU B:635 , LYS B:662 , HOH B:990
BINDING SITE FOR RESIDUE SO4 B 1047
2
AC2
SOFTWARE
ARG A:85 , TYR A:388 , ARG A:391 , GLU A:635 , LYS A:662
BINDING SITE FOR RESIDUE SO4 A 1048
3
AC3
SOFTWARE
HIS A:618 , CYS A:620 , GLU A:642 , CYS A:704 , HCS A:1049
BINDING SITE FOR RESIDUE ZN A 1051
4
AC4
SOFTWARE
HCS A:1050 , HIS B:618 , CYS B:620 , GLU B:642 , CYS B:704
BINDING SITE FOR RESIDUE ZN B 1052
5
AC5
SOFTWARE
ILE A:409 , GLY A:410 , SER A:411 , GLU A:462 , MSE A:529 , ASP A:577 , HIS A:618 , CYS A:620 , CYS A:704 , GLY A:705 , ZN A:1051
BINDING SITE FOR RESIDUE HCS A 1049
6
AC6
SOFTWARE
ILE B:409 , GLY B:410 , SER B:411 , GLU B:462 , MSE B:529 , ASP B:577 , HIS B:618 , CYS B:620 , CYS B:704 , GLY B:705 , ZN B:1052
BINDING SITE FOR RESIDUE HCS A 1050
7
AC7
SOFTWARE
PHE A:106 , LEU A:156 , ARG A:165 , CYS A:205 , HOH A:815
BINDING SITE FOR RESIDUE MRY A 1053
8
AC8
SOFTWARE
PHE B:106 , LEU B:156 , ARG B:165 , CYS B:205 , ILE B:587 , HOH B:915
BINDING SITE FOR RESIDUE MRY B 1054
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
Info
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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
(0, 0)
Info
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1xdjA02 (A:364-482,A:498-733)
1b: CATH_1xdjA01 (A:1-363,A:483-497)
1c: CATH_1xdjB01 (B:0-353,B:483-497)
1d: CATH_1xdjB02 (B:364-482,B:498-730)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
[code=3.20.20.210, no name defined]
(35)
Thermotoga maritima. Organism_taxid: 2336.
(6)
1a
1xdjA02
A:364-482,A:498-733
1b
1xdjA01
A:1-363,A:483-497
1c
1xdjB01
B:0-353,B:483-497
1d
1xdjB02
B:364-482,B:498-730
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Meth_synt_1_1xdjB01 (B:2-305)
1b: PFAM_Meth_synt_1_1xdjB02 (B:2-305)
2a: PFAM_Meth_synt_2_1xdjB03 (B:404-727)
2b: PFAM_Meth_synt_2_1xdjB04 (B:404-727)
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(
)
Clan
:
Methionine_synt
(18)
Family
:
Meth_synt_1
(4)
Thermotoga maritima
(2)
1a
Meth_synt_1-1xdjB01
B:2-305
1b
Meth_synt_1-1xdjB02
B:2-305
Family
:
Meth_synt_2
(5)
Thermotoga maritima
(2)
2a
Meth_synt_2-1xdjB03
B:404-727
2b
Meth_synt_2-1xdjB04
B:404-727
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Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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set fontsize 20
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wireframe 100
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Show PDB file:
Asym.Unit (243 KB)
Header - Asym.Unit
Biol.Unit 1 (121 KB)
Header - Biol.Unit 1
Biol.Unit 2 (119 KB)
Header - Biol.Unit 2
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