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SMTL ID : 7gxs.1
Crystal Structure of B-cell lymphoma 6 protein BTB domain in complex with ligand 9 at 5.68 MGy X-ray dose.
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.85 Å
Oligo State
homo-dimer
Ligands
2 x
ACE
-
TRP
-
VAL
-
ILE
-
PRO
-
ALA
:
WVIP tetrapeptide
(Non-covalent)
ACE-TRP-VAL-ILE-PRO-ALA.1:
12 residues within 4Å:
Chain A:
C.7
,
I.8
,
Q.9
,
F.10
,
T.11
Chain B:
F.88
,
R.93
,
L.94
,
H.115
,
V.116
,
T.119
Ligands:
DMS.4
16
PLIP interactions
:
6 interactions with chain B
,
10 interactions with chain A
Hydrophobic interactions:
B:F.88
,
B:L.94
,
B:L.94
,
B:T.119
,
A:I.8
,
A:I.8
,
A:Q.9
,
A:F.10
,
A:F.10
,
A:F.10
Water bridges:
B:R.93
,
B:T.119
Hydrogen bonds:
A:Q.9
,
A:Q.9
,
A:T.11
,
A:T.11
ACE-TRP-VAL-ILE-PRO-ALA.5:
12 residues within 4Å:
Chain A:
F.88
,
R.93
,
L.94
,
H.115
,
V.116
,
T.119
Chain B:
C.7
,
I.8
,
Q.9
,
F.10
,
T.11
Ligands:
DMS.8
16
PLIP interactions
:
10 interactions with chain B
,
6 interactions with chain A
Hydrophobic interactions:
B:I.8
,
B:I.8
,
B:Q.9
,
B:F.10
,
B:F.10
,
B:F.10
,
A:F.88
,
A:L.94
,
A:L.94
,
A:T.119
Hydrogen bonds:
B:Q.9
,
B:Q.9
,
B:T.11
,
A:T.119
Water bridges:
B:T.11
,
A:R.93
2 x 01:
(8S)-5-chloro-7-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]pyrazolo[1,5-a]pyrimidine-3-carbonitrile
01.2:
14 residues within 4Å:
Chain A:
M.50
,
A.51
,
C.52
,
S.53
,
G.54
,
Y.57
,
Q.112
,
M.113
,
E.114
Chain B:
N.20
,
R.23
,
L.24
,
R.27
,
I.29
12
PLIP interactions
:
10 interactions with chain A
,
2 interactions with chain B
Hydrophobic interactions:
A:Y.57
,
B:L.24
Hydrogen bonds:
A:M.50
,
A:G.54
,
A:E.114
,
B:R.27
Water bridges:
A:Y.57
,
A:Y.57
,
A:Q.112
,
A:H.115
pi-Stacking:
A:Y.57
,
A:Y.57
01.6:
14 residues within 4Å:
Chain A:
N.20
,
R.23
,
L.24
,
R.27
,
I.29
Chain B:
M.50
,
A.51
,
C.52
,
S.53
,
G.54
,
Y.57
,
Q.112
,
M.113
,
E.114
10
PLIP interactions
:
8 interactions with chain B
,
2 interactions with chain A
Hydrophobic interactions:
B:Y.57
,
A:L.24
Hydrogen bonds:
B:M.50
,
B:G.54
,
B:E.114
,
A:R.27
Water bridges:
B:Q.112
,
B:H.115
pi-Stacking:
B:Y.57
,
B:Y.57
2 x
CL
:
CHLORIDE ION
(Non-functional Binders)
CL.3:
4 residues within 4Å:
Chain A:
F.88
,
M.113
,
H.115
,
V.116
Ligand excluded by PLIP
CL.7:
4 residues within 4Å:
Chain B:
F.88
,
M.113
,
H.115
,
V.116
Ligand excluded by PLIP
2 x
DMS
:
DIMETHYL SULFOXIDE
(Non-functional Binders)
DMS.4:
4 residues within 4Å:
Chain A:
I.8
Ligands:
ACE-TRP-VAL-ILE-PRO-ALA.1
,
ACE-TRP-VAL-ILE-PRO-ALA.1
,
ACE-TRP-VAL-ILE-PRO-ALA.1
No protein-ligand interaction detected (PLIP)
DMS.8:
4 residues within 4Å:
Chain B:
I.8
Ligands:
ACE-TRP-VAL-ILE-PRO-ALA.5
,
ACE-TRP-VAL-ILE-PRO-ALA.5
,
ACE-TRP-VAL-ILE-PRO-ALA.5
No protein-ligand interaction detected (PLIP)
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Rodrigues, M.J. et al., Specific radiation damage to halogenated inhibitors and ligands in protein-ligand crystal structures. J.Appl.Crystallogr. (2024)
Release Date
2024-12-11
Peptides
B-cell lymphoma 6 protein:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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B-cell lymphoma 6 protein
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Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog
Background
Transparent
Resolution
Low
Medium
High
Extreme