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SMTL ID : 5akp.1
Crystal structure of the dark-adapted full-length bacteriophytochrome XccBphP from Xanthomonas campestris bound to BV chromophore
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 3.25 Å
Oligo State
homo-dimer
Ligands
2 x
BLA
:
BILIVERDINE IX ALPHA
(Covalent)
(Non-covalent)
BLA.1:
23 residues within 4Å:
Chain A:
C.19
,
I.24
,
M.172
,
I.184
,
Y.196
,
Y.201
,
S.204
,
D.205
,
I.206
,
P.207
,
A.210
,
Y.214
,
R.220
,
R.252
,
V.254
,
S.255
,
V.257
,
H.258
,
Y.261
,
T.270
,
V.272
,
S.286
,
H.288
19
PLIP interactions
:
19 interactions with chain A
Hydrophobic interactions:
A:I.184
,
A:Y.196
,
A:Y.201
,
A:Y.201
,
A:A.210
,
A:V.257
,
A:Y.261
,
A:T.270
,
A:V.272
,
A:V.272
Hydrogen bonds:
A:Y.214
,
A:S.255
,
A:T.270
,
A:S.286
Salt bridges:
A:R.220
,
A:R.252
,
A:H.258
,
A:H.288
pi-Stacking:
A:Y.201
BLA.4:
24 residues within 4Å:
Chain B:
C.19
,
I.24
,
M.172
,
Y.174
,
I.184
,
Y.201
,
S.204
,
D.205
,
I.206
,
P.207
,
A.210
,
Y.214
,
R.220
,
R.252
,
V.254
,
S.255
,
V.257
,
H.258
,
Y.261
,
L.262
,
T.270
,
V.272
,
S.286
,
H.288
21
PLIP interactions
:
21 interactions with chain B
Hydrophobic interactions:
B:Y.174
,
B:I.184
,
B:Y.201
,
B:Y.201
,
B:Y.201
,
B:I.206
,
B:A.210
,
B:V.257
,
B:V.272
,
B:V.272
Hydrogen bonds:
B:Y.214
,
B:S.255
,
B:T.270
,
B:S.286
Water bridges:
B:D.205
,
B:H.258
Salt bridges:
B:R.220
,
B:R.252
,
B:H.258
,
B:H.288
pi-Stacking:
B:Y.201
2 x
TRS
:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
(Non-functional Binders)
TRS.2:
4 residues within 4Å:
Chain A:
D.177
,
E.178
,
W.180
,
L.281
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:W.180
,
A:W.180
,
A:L.281
TRS.5:
6 residues within 4Å:
Chain B:
F.176
,
D.177
,
E.178
,
W.180
,
L.281
,
W.282
2
PLIP interactions
:
2 interactions with chain B
Hydrogen bonds:
B:D.177
,
B:L.281
1 x
CL
:
CHLORIDE ION
(Non-functional Binders)
CL.3:
1 residues within 4Å:
Chain A:
D.245
Ligand excluded by PLIP
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Otero, L.H. et al., Structure of the Full-Length Bacteriophytochrome from the Plant Pathogen Xanthomonas Campestris Provides Clues to its Long-Range Signaling Mechanism. J.Mol.Biol. (2016)
Release Date
2016-05-04
Peptides
PHYTOCHROME-LIKE PROTEIN:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
Export Alignment
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Clustal Format
PNG Image
Secondary Structure
None
DSSP
PSIPRED
SSpro
Colour Scheme
Fade Mismatches
Enhance Mismatches
Chain
Unique Chain
Rainbow
2° Structure
Bfactor
Bfactor Range
SOA
Entropy
Clustal
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Size
Charged
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Proline
Ser/Thr
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PHYTOCHROME-LIKE PROTEIN
Related Entries With Identical Sequence
6pl0.1
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog
Background
Transparent
Resolution
Low
Medium
High
Extreme