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SMTL ID : 8csf.1
(1 other biounit)
WbbB D232C-Kdo adduct + alpha-Rha(1,3)GlcNAc ternary complex
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.40 Å
Oligo State
homo-dimer
Ligands
2 x
NAG
-
RAM
:
alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
(Non-covalent)
NAG-RAM.1:
12 residues within 4Å:
Chain A:
R.13
,
P.18
,
Y.19
,
W.21
,
W.55
,
L.65
,
E.159
,
I.160
,
R.164
,
V.230
,
G.268
Ligands:
KDO.5
6
PLIP interactions
:
6 interactions with chain A
Hydrophobic interactions:
A:L.65
,
A:I.160
Hydrogen bonds:
A:R.164
,
A:R.13
,
A:R.13
,
A:W.21
,
A:E.159
Water bridges:
A:Y.19
,
A:Y.19
NAG-RAM.6:
12 residues within 4Å:
Chain B:
R.13
,
P.18
,
Y.19
,
W.21
,
W.55
,
L.65
,
E.159
,
I.160
,
R.164
,
V.230
,
G.268
Ligands:
KDO.10
6
PLIP interactions
:
6 interactions with chain B
Hydrophobic interactions:
B:L.65
,
B:I.160
Hydrogen bonds:
B:R.164
,
B:R.13
,
B:R.13
,
B:W.21
,
B:E.159
Water bridges:
B:Y.19
,
B:S.234
2 x
C5P
:
CYTIDINE-5'-MONOPHOSPHATE
(Non-covalent)
C5P.2:
14 residues within 4Å:
Chain A:
P.162
,
R.164
,
V.227
,
L.228
,
Q.229
,
R.264
,
A.265
,
H.266
,
P.267
,
S.286
,
S.301
,
S.302
,
V.303
Ligands:
KDO.5
16
PLIP interactions
:
16 interactions with chain A
Hydrophobic interactions:
A:V.227
,
A:V.303
Hydrogen bonds:
A:P.162
,
A:L.228
,
A:L.228
,
A:Q.229
,
A:R.264
,
A:S.286
,
A:S.286
,
A:S.286
,
A:S.302
Water bridges:
A:V.230
,
A:H.266
,
A:N.300
Salt bridges:
A:R.164
,
A:H.266
C5P.7:
14 residues within 4Å:
Chain B:
P.162
,
R.164
,
V.227
,
L.228
,
Q.229
,
R.264
,
A.265
,
H.266
,
P.267
,
S.286
,
S.301
,
S.302
,
V.303
Ligands:
KDO.10
16
PLIP interactions
:
16 interactions with chain B
Hydrophobic interactions:
B:V.227
,
B:V.303
Hydrogen bonds:
B:P.162
,
B:L.228
,
B:L.228
,
B:Q.229
,
B:R.264
,
B:S.286
,
B:S.286
,
B:S.286
,
B:S.302
Water bridges:
B:V.230
,
B:H.266
,
B:N.300
Salt bridges:
B:R.164
,
B:H.266
4 x
NA
:
SODIUM ION
(Non-functional Binders)
NA.3:
2 residues within 4Å:
Chain A:
N.326
,
L.328
1
PLIP interactions
:
1 interactions with chain A
Hydrogen bonds:
A:N.326
NA.4:
3 residues within 4Å:
Chain A:
N.207
,
L.210
,
E.404
1
PLIP interactions
:
1 interactions with chain A
Hydrogen bonds:
A:E.404
NA.8:
2 residues within 4Å:
Chain B:
N.326
,
L.328
1
PLIP interactions
:
1 interactions with chain B
Water bridges:
B:N.326
NA.9:
3 residues within 4Å:
Chain B:
N.207
,
L.210
,
E.404
1
PLIP interactions
:
1 interactions with chain B
Hydrogen bonds:
B:E.404
2 x
KDO
:
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid
(Post Translational Modification)
KDO.5:
13 residues within 4Å:
Chain A:
R.13
,
E.159
,
I.160
,
R.164
,
N.180
,
V.230
,
C.233
,
S.234
,
N.235
,
H.266
Ligands:
NAG-RAM.1
,
NAG-RAM.1
,
C5P.2
11
PLIP interactions
:
11 interactions with chain A
Hydrogen bonds:
A:E.159
,
A:R.164
,
A:R.164
,
A:N.180
,
A:N.180
,
A:S.234
,
A:N.235
,
A:H.266
Water bridges:
A:S.234
,
A:S.234
Salt bridges:
A:R.13
KDO.10:
13 residues within 4Å:
Chain B:
R.13
,
E.159
,
I.160
,
R.164
,
N.180
,
V.230
,
C.233
,
S.234
,
N.235
,
H.266
Ligands:
NAG-RAM.6
,
NAG-RAM.6
,
C5P.7
11
PLIP interactions
:
11 interactions with chain B
Hydrogen bonds:
B:E.159
,
B:R.164
,
B:R.164
,
B:N.180
,
B:N.180
,
B:S.234
,
B:N.235
,
B:H.266
Water bridges:
B:S.234
,
B:S.234
Salt bridges:
B:R.13
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Forrester, T.J.B. et al., The retaining beta-Kdo glycosyltransferase WbbB uses a double-displacement mechanism with an intermediate adduct rearrangement step. Nat Commun (2022)
Release Date
2022-11-09
Peptides
N-acetyl glucosaminyl transferase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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N-acetyl glucosaminyl transferase
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8csd.1
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8csd.2
|
8csf.2
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