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SMTL ID : 6i7f.1
Dehaloperoxidase B from Amphitrite ornata - complex with 2,4-dichlorophenol
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.85 Å
Oligo State
homo-dimer
Ligands
2 x
HEM
:
PROTOPORPHYRIN IX CONTAINING FE
(Non-covalent)
HEM.1:
20 residues within 4Å:
Chain A:
F.24
,
E.31
,
N.34
,
F.35
,
D.54
,
H.55
,
K.58
,
V.59
,
L.62
,
M.63
,
L.83
,
M.86
,
Q.88
,
H.89
,
L.92
,
N.96
,
F.97
,
L.100
,
L.127
Ligands:
5JC.2
20
PLIP interactions
:
20 interactions with chain A
,
Hydrophobic interactions:
A:F.24
,
A:F.35
,
A:F.35
,
A:K.58
,
A:V.59
,
A:V.59
,
A:L.62
,
A:L.62
,
A:L.83
,
A:Q.88
,
A:L.92
,
A:N.96
,
A:F.97
,
A:F.97
,
A:L.100
,
A:L.127
Hydrogen bonds:
A:H.55
Salt bridges:
A:K.58
pi-Stacking:
A:H.55
Metal complexes:
A:H.89
HEM.5:
18 residues within 4Å:
Chain B:
F.24
,
E.31
,
N.34
,
F.35
,
H.55
,
K.58
,
V.59
,
L.62
,
M.63
,
L.83
,
M.86
,
Q.88
,
H.89
,
L.92
,
N.96
,
F.97
,
L.127
Ligands:
5JC.6
14
PLIP interactions
:
14 interactions with chain B
,
Hydrophobic interactions:
B:F.24
,
B:F.35
,
B:F.35
,
B:V.59
,
B:L.62
,
B:L.62
,
B:L.83
,
B:Q.88
,
B:L.92
,
B:N.96
,
B:L.127
Salt bridges:
B:H.55
,
B:H.55
Metal complexes:
B:H.89
2 x
5JC
:
2,4-dichlorophenol
(Non-covalent)
5JC.2:
9 residues within 4Å:
Chain A:
A.17
,
F.21
,
F.35
,
H.55
,
T.56
,
V.59
,
F.60
,
L.100
Ligands:
HEM.1
5
PLIP interactions
:
5 interactions with chain A
Hydrophobic interactions:
A:F.21
,
A:T.56
,
A:V.59
,
A:L.100
pi-Stacking:
A:F.21
5JC.6:
9 residues within 4Å:
Chain B:
A.17
,
F.21
,
F.35
,
H.55
,
T.56
,
V.59
,
F.60
,
L.100
Ligands:
HEM.5
4
PLIP interactions
:
4 interactions with chain B
Hydrophobic interactions:
B:F.21
,
B:V.59
,
B:L.100
pi-Stacking:
B:F.21
2 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.3:
4 residues within 4Å:
Chain A:
G.1
,
F.2
,
K.3
,
D.116
6
PLIP interactions
:
6 interactions with chain A
Hydrogen bonds:
A:F.2
,
A:K.3
,
A:D.116
Water bridges:
A:G.1
,
A:Q.4
,
A:S.119
SO4.4:
3 residues within 4Å:
Chain A:
K.32
,
V.39
,
G.40
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:G.40
Water bridges:
A:K.32
,
A:K.32
Salt bridges:
A:K.32
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Moreno-Chicano, T. et al., High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography. Iucrj (2019)
Release Date
2019-11-20
Peptides
Dehaloperoxidase B:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Secondary Structure
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Enhance Mismatches
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2° Structure
Bfactor
Bfactor Range
SOA
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Dehaloperoxidase B
Toggle Identical (AB)
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6vd3.1
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6vd4.1
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6vd4.2
|
6vd5.1
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6vd5.2
|
6vd6.1
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6vd6.2
|
6vdr.1
|
6vdr.2
|
6vds.1
|
6vds.2
|
6vdt.1
|
6vdt.2
|
6vdu.1
|
6vdu.2
|
6vdv.1
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6vdv.2
|
6vdw.1
|
6vdw.2
|
6vdx.1
|
6vdx.2
|
6vdy.1
|
6vdy.2
|
7jor.1
|
7jor.2
|
7kcu.1
|
7kcu.2
|
7kfm.1
|
7lzk.1
|
7lzk.2
|
7lzn.1
|
7lzn.2
|
7lzo.1
|
7lzo.2
|
7m0f.1
|
7m0f.2
|
7m0h.1
|
7m0h.2
|
7m1i.1
|
7m1i.2
|
7m1j.1
|
7m1j.2
|
7m1k.1
|
7m1k.2
|
7sjb.1
|
7sjb.2
|
7sjc.1
|
7sjc.2
|
7sjd.1
|
7sjd.2
|
7sje.1
|
7sje.2
|
7sjf.1
|
7sjf.2
|
7sjg.1
|
7sjg.2
|
7sjh.1
|
7sjh.2
|
7sji.1
|
7sji.2
|
7t9c.1
|
7t9c.2
|
7t9d.1
|
7t9d.2
|
7t9e.1
|
7t9e.2
|
8dog.1
|
8dog.2
|
8doh.1
|
8doh.2
|
8doi.1
|
8doi.2
|
8doj.1
|
8doj.2
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog
Background
Transparent
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