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3GA6
Asym. Unit
Info
Asym.Unit (210 KB)
Biol.Unit 1 (103 KB)
Biol.Unit 2 (104 KB)
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(1)
Title
:
MTH0212 IN COMPLEX WITH TWO DNA HELICES
Authors
:
K. Lakomek, A. Dickmanns, R. Ficner
Date
:
16 Feb 09 (Deposition) - 09 Mar 10 (Release) - 12 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,D,F,G,H
Biol. Unit 1: A,D,F (1x)
Biol. Unit 2: B,G,H (1x)
Keywords
:
Protein-Dna Complex, Twin, Disorder Of Dna, 3'-5' Exonuclease, Ap Endonuclease, 2'-Desoxyuridine Endonuclease, Hydrolase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Lakomek, A. Dickmanns, E. Ciirdaeva, L. Schomacher, R. Ficner
Crystal Structure Analysis Of Dna Uridine Endonuclease Mth212 Bound To Dna
J. Mol. Biol. V. 399 604 2010
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 24)
Info
All Hetero Components
1a: (DUa)
1b: (DUb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
2s: GLYCEROL (GOLs)
3a: SODIUM ION (NAa)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DU
2
Mod. Residue
2
GOL
19
Ligand/Ion
GLYCEROL
3
NA
1
Ligand/Ion
SODIUM ION
4
PO4
2
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(21, 21)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:1088 , ALA A:1131 , GLU A:1134 , ARG B:2090 , HOH B:9027
BINDING SITE FOR RESIDUE GOL A 7002
02
AC2
SOFTWARE
MET A:1027 , GLU A:1054 , GLY A:1055 , LYS A:1076
BINDING SITE FOR RESIDUE GOL A 7004
03
AC3
SOFTWARE
LEU A:1004 , ILE A:1033 , VAL A:1077 , PHE A:1102 , NA A:7401
BINDING SITE FOR RESIDUE GOL A 7006
04
AC4
SOFTWARE
LYS A:1020 , ASP A:1242 , MET A:1244 , HOH A:9105
BINDING SITE FOR RESIDUE GOL A 7010
05
AC5
SOFTWARE
VAL A:1176 , ALA A:1179 , TRP A:1180 , LYS A:1183 , HOH A:9199 , HOH A:9219
BINDING SITE FOR RESIDUE GOL A 7012
06
AC6
SOFTWARE
HOH A:459 , LYS A:1183 , GLU A:1186 , ASN A:1187 , GLU B:2054 , HOH B:9172
BINDING SITE FOR RESIDUE GOL A 7013
07
AC7
SOFTWARE
PRO A:1043 , GLU A:1044 , LEU A:1046 , ARG A:1051 , GLU B:2228 , GLU B:2229 , HOH B:9174
BINDING SITE FOR RESIDUE GOL A 7015
08
AC8
SOFTWARE
GLY A:1055 , TYR A:1056 , ARG A:1057 , LYS A:1076 , ASP B:2182 , GLU B:2186
BINDING SITE FOR RESIDUE GOL A 7020
09
AC9
SOFTWARE
ASP A:1103 , ASP A:1104
BINDING SITE FOR RESIDUE GOL A 7024
10
BC1
SOFTWARE
ARG A:1090 , GLU A:1120 , LYS A:1123 , TYR A:1124 , GLU A:1127 , ARG B:2138
BINDING SITE FOR RESIDUE GOL A 7030
11
BC2
SOFTWARE
HOH A:443 , ILE A:1185 , TYR A:1189 , VAL A:1190 , ASP A:1191 , ARG A:1194 , HOH A:9268
BINDING SITE FOR RESIDUE GOL A 7031
12
BC3
SOFTWARE
ASP A:1032 , THR A:1075 , LYS A:1076 , VAL A:1077 , GOL A:7006 , HOH A:9008
BINDING SITE FOR RESIDUE NA A 7401
13
BC4
SOFTWARE
GLU B:2094 , GLU B:2120 , ARG B:2121 , HOH B:9353
BINDING SITE FOR RESIDUE GOL B 7003
14
BC5
SOFTWARE
GLY A:1087 , VAL A:1088 , GLU A:1089 , GLY B:2087 , VAL B:2088 , GLU B:2089 , ASP B:2092 , HOH B:9144 , HOH B:9194
BINDING SITE FOR RESIDUE GOL B 7011
15
BC6
SOFTWARE
GLU B:2158 , ILE B:2159 , LEU B:2161 , PRO B:2164 , PRO B:2200 , HOH B:9118 , HOH B:9167 , HOH B:9306
BINDING SITE FOR RESIDUE GOL B 7021
16
BC7
SOFTWARE
ASN B:2114 , LYS B:2116 , LYS B:2125 , ASN B:2153 , SER B:2171 , GLY B:2172 , LEU B:2221 , HOH B:9222
BINDING SITE FOR RESIDUE GOL B 7022
17
BC8
SOFTWARE
PRO B:2062 , GLU B:2084 , HOH B:9090 , HOH B:9109
BINDING SITE FOR RESIDUE GOL B 7027
18
BC9
SOFTWARE
SER B:2168 , ASN B:2169 , PRO B:2175 , HOH B:9014
BINDING SITE FOR RESIDUE GOL B 7032
19
CC1
SOFTWARE
ASP B:2191 , THR B:2192 , PHE B:2193 , ARG B:2220 , ASP B:2222 , TYR B:2223 , PHE B:2224 , TRP B:2238 , ILE B:2239 , ILE B:2251 , HOH B:9377
BINDING SITE FOR RESIDUE GOL B 7033
20
CC2
SOFTWARE
LEU B:2082 , ARG B:2083
BINDING SITE FOR RESIDUE PO4 B 7204
21
CC3
SOFTWARE
ASP B:2104 , LYS B:2233 , ILE B:2255 , GLU B:2256
BINDING SITE FOR RESIDUE PO4 B 7205
[
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]
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
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Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3ga6a_ (A:)
1b: SCOP_d3ga6b_ (B:)
View:
Select:
Label:
Classes
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)
(
)
Folds
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(
)
Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
DNase I-like
(70)
Superfamily
:
DNase I-like
(70)
Family
:
automated matches
(26)
Protein domain
:
automated matches
(26)
Methanothermobacter thermautotrophicus [TaxId: 187420]
(15)
1a
d3ga6a_
A:
1b
d3ga6b_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain D
Chain F
Chain G
Chain H
Asymmetric Unit 1
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Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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Show PDB file:
Asym.Unit (210 KB)
Header - Asym.Unit
Biol.Unit 1 (103 KB)
Header - Biol.Unit 1
Biol.Unit 2 (104 KB)
Header - Biol.Unit 2
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