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SMTL ID : 8csb.2
(1 other biounit)
WbbB D232N in complex with CMP-beta-Kdo
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.25 Å
Oligo State
homo-dimer
Ligands
2 x
PO4
:
PHOSPHATE ION
(Non-functional Binders)
PO4.1:
5 residues within 4Å:
Chain A:
R.13
,
E.159
,
N.233
,
S.234
Ligands:
CMK.2
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:E.159
,
A:N.233
,
A:S.234
Salt bridges:
A:R.13
PO4.4:
5 residues within 4Å:
Chain B:
R.13
,
E.159
,
N.233
,
S.234
Ligands:
CMK.5
5
PLIP interactions
:
5 interactions with chain B
Hydrogen bonds:
B:E.159
,
B:E.159
,
B:N.233
,
B:S.234
Salt bridges:
B:R.13
2 x
CMK
:
CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID
(Non-covalent)
CMK.2:
22 residues within 4Å:
Chain A:
E.159
,
I.160
,
P.162
,
R.164
,
N.180
,
V.227
,
L.228
,
Q.229
,
V.230
,
N.233
,
S.234
,
N.235
,
R.264
,
A.265
,
H.266
,
P.267
,
S.286
,
S.301
,
S.302
,
V.303
Ligands:
PO4.1
,
C5P.3
21
PLIP interactions
:
21 interactions with chain A
Hydrophobic interactions:
A:V.227
,
A:V.230
,
A:V.303
Hydrogen bonds:
A:R.164
,
A:R.164
,
A:N.180
,
A:L.228
,
A:L.228
,
A:Q.229
,
A:V.230
,
A:N.233
,
A:N.235
,
A:R.264
,
A:S.286
,
A:S.286
,
A:S.301
,
A:S.302
Water bridges:
A:S.286
Salt bridges:
A:R.164
,
A:H.266
,
A:H.266
CMK.5:
22 residues within 4Å:
Chain B:
E.159
,
I.160
,
P.162
,
R.164
,
N.180
,
V.227
,
L.228
,
Q.229
,
V.230
,
N.233
,
S.234
,
N.235
,
R.264
,
A.265
,
H.266
,
P.267
,
S.286
,
S.301
,
S.302
,
V.303
Ligands:
PO4.4
,
C5P.6
22
PLIP interactions
:
22 interactions with chain B
Hydrophobic interactions:
B:V.227
,
B:V.230
,
B:V.303
Hydrogen bonds:
B:E.159
,
B:R.164
,
B:R.164
,
B:N.180
,
B:L.228
,
B:L.228
,
B:Q.229
,
B:V.230
,
B:N.233
,
B:N.235
,
B:R.264
,
B:S.286
,
B:S.286
,
B:S.301
,
B:S.302
Water bridges:
B:S.286
Salt bridges:
B:R.164
,
B:H.266
,
B:H.266
2 x
C5P
:
CYTIDINE-5'-MONOPHOSPHATE
(Non-covalent)
C5P.3:
14 residues within 4Å:
Chain A:
R.164
,
V.227
,
L.228
,
Q.229
,
R.264
,
A.265
,
H.266
,
P.267
,
S.286
,
S.301
,
S.302
,
V.303
,
E.306
Ligands:
CMK.2
12
PLIP interactions
:
12 interactions with chain A
Hydrophobic interactions:
A:V.227
,
A:H.266
,
A:V.303
Hydrogen bonds:
A:L.228
,
A:L.228
,
A:R.264
,
A:S.286
,
A:S.286
,
A:S.302
Water bridges:
A:S.286
Salt bridges:
A:R.164
,
A:H.266
C5P.6:
14 residues within 4Å:
Chain B:
R.164
,
V.227
,
L.228
,
Q.229
,
R.264
,
A.265
,
H.266
,
P.267
,
S.286
,
S.301
,
S.302
,
V.303
,
E.306
Ligands:
CMK.5
12
PLIP interactions
:
12 interactions with chain B
Hydrophobic interactions:
B:V.227
,
B:H.266
,
B:V.303
Hydrogen bonds:
B:L.228
,
B:L.228
,
B:R.264
,
B:S.286
,
B:S.286
,
B:S.302
Water bridges:
B:S.286
Salt bridges:
B:R.164
,
B:H.266
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
B
B
B
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N-acetyl glucosaminyl transferase
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Related Entries With Identical Sequence
8csb.1
|
8csc.1
|
8csc.2
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