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SMTL ID : 3twp.1
(1 other biounit)
Crystal structure of M. tuberculosis TrpD in complex with an inhibitor
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.83 Å
Oligo State
homo-dimer
Ligands
2 x
PRP
:
1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose
(Non-covalent)
PRP.1:
20 residues within 4Å:
Chain A:
V.105
,
G.106
,
G.108
,
G.109
,
N.116
,
L.117
,
S.118
,
T.119
,
K.134
,
N.137
,
R.138
,
A.139
,
A.140
,
S.141
,
S.142
,
G.145
,
G.146
,
E.251
Ligands:
MG.2
,
MG.3
25
PLIP interactions
:
25 interactions with chain A
Hydrogen bonds:
A:G.106
,
A:G.109
,
A:N.116
,
A:L.117
,
A:S.118
,
A:S.118
,
A:T.119
,
A:N.137
,
A:N.137
,
A:A.140
,
A:S.141
,
A:S.142
,
A:G.146
Water bridges:
A:G.106
,
A:G.108
,
A:G.108
,
A:G.108
,
A:D.110
,
A:S.141
,
A:S.141
,
A:A.147
,
A:A.147
,
A:R.192
,
A:R.192
Salt bridges:
A:K.134
PRP.6:
20 residues within 4Å:
Chain B:
V.105
,
G.106
,
G.108
,
G.109
,
N.116
,
L.117
,
S.118
,
T.119
,
K.134
,
N.137
,
R.138
,
A.139
,
A.140
,
S.141
,
S.142
,
G.145
,
G.146
,
E.251
Ligands:
MG.7
,
MG.8
22
PLIP interactions
:
22 interactions with chain B
Hydrogen bonds:
B:G.106
,
B:G.109
,
B:N.116
,
B:L.117
,
B:S.118
,
B:S.118
,
B:T.119
,
B:N.137
,
B:N.137
,
B:A.140
,
B:S.141
,
B:S.142
,
B:S.142
,
B:G.146
Water bridges:
B:G.106
,
B:T.107
,
B:T.107
,
B:T.114
,
B:A.147
,
B:A.147
,
B:R.192
Salt bridges:
B:K.134
4 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.2:
5 residues within 4Å:
Chain A:
G.106
,
S.118
,
E.251
Ligands:
PRP.1
,
MG.3
4
PLIP interactions
:
2 interactions with chain A
,
2 Ligand-Water interactions
Metal complexes:
A:S.118
,
A:E.251
,
H
2
O.4
,
H
2
O.5
MG.3:
5 residues within 4Å:
Chain A:
D.110
,
D.250
,
E.251
Ligands:
PRP.1
,
MG.2
5
PLIP interactions
:
2 interactions with chain A
,
3 Ligand-Water interactions
Metal complexes:
A:D.250
,
A:E.251
,
H
2
O.3
,
H
2
O.5
,
H
2
O.11
MG.7:
5 residues within 4Å:
Chain B:
G.106
,
S.118
,
E.251
Ligands:
PRP.6
,
MG.8
4
PLIP interactions
:
2 interactions with chain B
,
2 Ligand-Water interactions
Metal complexes:
B:S.118
,
B:E.251
,
H
2
O.12
,
H
2
O.15
MG.8:
4 residues within 4Å:
Chain B:
D.250
,
E.251
Ligands:
PRP.6
,
MG.7
5
PLIP interactions
:
2 interactions with chain B
,
3 Ligand-Water interactions
Metal complexes:
B:D.250
,
B:E.251
,
H
2
O.14
,
H
2
O.15
,
H
2
O.17
2 x
SAL
:
2-HYDROXYBENZOIC ACID
(Non-covalent)
SAL.4:
9 residues within 4Å:
Chain A:
N.137
,
A.178
,
P.179
,
H.182
,
P.183
,
Y.185
,
R.186
,
A.189
,
R.193
5
PLIP interactions
:
5 interactions with chain A
Hydrophobic interactions:
A:P.179
,
A:R.186
,
A:A.189
Hydrogen bonds:
A:N.137
,
A:R.193
SAL.9:
8 residues within 4Å:
Chain B:
N.137
,
A.178
,
P.179
,
H.182
,
Y.185
,
R.186
,
A.189
,
R.193
5
PLIP interactions
:
5 interactions with chain B
Hydrophobic interactions:
B:P.179
,
B:P.179
,
B:R.186
Hydrogen bonds:
B:N.137
,
B:R.193
1 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.5:
7 residues within 4Å:
Chain A:
A.140
,
S.141
,
R.192
,
G.196
,
V.197
,
P.198
,
N.202
6
PLIP interactions
:
6 interactions with chain A
Hydrogen bonds:
A:R.192
,
A:R.192
,
A:V.197
,
A:N.202
Water bridges:
A:A.140
,
A:G.196
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Castell, A. et al., The Substrate Capture Mechanism of Mycobacterium tuberculosis Anthranilate Phosphoribosyltransferase Provides a Mode for Inhibition. Biochemistry (2013)
Release Date
2012-09-26
Peptides
Anthranilate phosphoribosyltransferase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
C
B
A
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Anthranilate phosphoribosyltransferase
Toggle Identical (AB)
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|
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3qs8.1
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|
3r6c.1
|
3r6c.2
|
3r88.1
|
3twp.2
|
3uu1.1
|
3uu1.2
|
3uu1.3
|
3uu1.4
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