0.015537
0.008970
0.000000
0.000000
0.017940
0.000000
0.000000
0.000000
0.011887
0.00000
0.00000
0.00000
Lehmann, C.
Vertessy, L.
Sheldrick, G.M.
Dauter, Z.
Dauter, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
48
90.00
90.00
120.00
64.364
64.364
84.128
C8 H9 N O4
183.161
(2S)-amino(3,5-dihydroxyphenyl)ethanoic acid
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C6 H12 O6
180.156
beta-D-glucopyranose
D-saccharide, beta linking
C7 H15 N O3
161.199
4-epi-vancosamine
4-EPI-VANCOSAMINE
L-saccharide, alpha linking
C8 H9 N O3
167.162
(2R)-amino(4-hydroxyphenyl)ethanoic acid
D-peptide linking
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
H2 O
18.015
WATER
non-polymer
C7 H15 N O2
145.199
N-methyl-D-leucine
D-peptide linking
C9 H11 N O4
197.188
n
(betaR)-beta-hydroxy-L-Tyrosine
L-peptide linking
C9 H10 Cl N O4
231.633
(betaR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
D-peptide linking
C6 H12 O5
164.156
alpha-L-rhamnopyranose
L-saccharide, alpha linking
SZ
Helv.Chim.Acta
HCACAV
0010
0018-019X
86
1478
10.1002/HLCA.200390131
Structures of Four Crystal Forms of Decaplanin
2003
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
CCD
1999-10-15
CHESS
MAD
M
x-ray
1
0.98000
1.0
0.98500
1.0
X9B
NSLS
0.98000,0.98500
SYNCHROTRON
NSLS BEAMLINE X9B
1115.532
DECAPLANIN
4
nat
polymer
326.297
alpha-L-rhamnopyranose-(1-2)-beta-D-glucopyranose
4
man
branched
161.199
4-epi-vancosamine
4
man
non-polymer
92.094
GLYCEROL
2
syn
non-polymer
18.015
water
73
nat
water
M86-1410
no
yes
(MLU)(OMZ)N(GHP)(GHP)(OMX)(3FG)
XXNGGYX
A,B,C,D
polypeptide(L)
n
n
n
n
n
n
n
CULTURE HIL Y-86, 36910
sample
100235
UNCULTURED ACTINOMYCETE
DSM 4763
1
3.93
57.61
8.50
0.1M TRIS, PH=8.5, 44% MGSO4, pH 8.50
entity_poly
pdbx_database_proc
pdbx_database_status
pdbx_seq_map_depositor_info
struct_conn
atom_site
chem_comp
entity
pdbx_branch_scheme
pdbx_chem_comp_identifier
pdbx_database_status
pdbx_entity_branch
pdbx_entity_branch_descriptor
pdbx_entity_branch_link
pdbx_entity_branch_list
pdbx_entity_nonpoly
pdbx_molecule
pdbx_nonpoly_scheme
pdbx_struct_assembly_gen
pdbx_struct_special_symmetry
struct_asym
struct_conn
struct_site
struct_site_gen
repository
Initial release
Carbohydrate remediation
repository
Remediation
Atomic model
Database references
Derived calculations
Structure summary
Version format compliance
Other
Other
Non-polymer description
Data collection
Derived calculations
Other
Polymer sequence
Atomic model
Data collection
Derived calculations
Other
Structure summary
1
0
2005-07-11
1
1
2011-07-13
1
2
2012-07-11
1
3
2012-11-30
1
4
2013-05-01
2
0
2019-04-24
3
0
2020-07-29
_entity_poly.pdbx_seq_one_letter_code_can
_pdbx_database_status.recvd_author_approval
_pdbx_seq_map_depositor_info.one_letter_code
_struct_conn.pdbx_leaving_atom_flag
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.label_alt_id
_atom_site.label_asym_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_entity_id
_atom_site.occupancy
_atom_site.type_symbol
_chem_comp.name
_chem_comp.type
_pdbx_database_status.status_code_sf
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_special_symmetry.label_asym_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
A
BGC
9
n
E
BGC
1
A
RAM
10
n
E
RAM
2
B
BGC
9
n
F
BGC
1
B
RAM
10
n
F
RAM
2
C
BGC
9
n
G
BGC
1
C
RAM
10
n
G
RAM
2
D
BGC
9
n
H
BGC
1
D
RAM
10
n
H
RAM
2
DGlcpb
b-D-glucopyranose
b-D-Glcp
Glc
LRhapa
a-L-rhamnopyranose
a-L-Rhap
Rha
CRYSTAL STRUCTURE OF DECAPLANIN - SPACE GROUP P21
CRYSTAL STRUCTURE OF DECAPLANIN - SPACE GROUP P21, SECOND FORM
CRYSTAL STRUCTURE OF DECAPLANIN - SPACE GROUP P6122, SECOND FORM
PDBE
Y
PDBE
2000-12-22
REL
REL
1
D
O
HOH
2001
6.06
oligosaccharide
LRhapa1-2DGlcpb1-ROH
2
GMML
1.0
Glycam Condensed Sequence
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2211m-1a_1-5]/1-2/a2-b1
2
PDB2Glycan
1.1.0
WURCS
[][D-1-deoxy-Glcp]{[(2+1)][a-L-Rhap]{}}
2
PDB-CARE
LINUCS
C1
O2
RAM
BGC
2
1
2
O1
HO2
sing
n
n
ERE
4-epi-vancosamine
GOL
GLYCEROL
HOH
water
DECAPLANIN IS A TRICYCLIC GLYCOPEPTIDE.
HERE, DECAPLANIN IS REPRESENTED BY GROUPING TOGETHER THE
SEQUENCE (SEQRES) AND THE THREE LIGANDS (HET) BGC, ERE AND RAM.
GROUP: 1
NAME: DECAPLANIN
CHAIN: A, B, C, D
COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 7
COMPONENT_2: SUGAR RESIDUES 8, 9 AND 10
DESCRIPTION: DECAPLANIN IS A TRICYCLIC GLYCOPEPTIDE.
THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE
CONFIGURATION D-D-L-D-D-L-L, GLYCOSYLATED
BY A MONOSACCHARIDE AND A DISACCHARIDE
Antibiotic
DECAPLANIN IS A TRICYCLIC GLYCOPEPTIDE.
THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE
CONFIGURATION D-D-L-D-D-L-L, GLYCOSYLATED
Decaplanin
Glycopeptide
ERE
8
3
ERE
ERE
8
A
ERE
8
3
ERE
ERE
8
B
GOL
1002
4
GOL
GOL
1002
B
ERE
8
3
ERE
ERE
8
C
ERE
8
3
ERE
ERE
8
D
GOL
1001
4
GOL
GOL
1001
D
HOH
2001
5
HOH
HOH
2001
A
HOH
2002
5
HOH
HOH
2002
A
HOH
2003
5
HOH
HOH
2003
A
HOH
2004
5
HOH
HOH
2004
A
HOH
2005
5
HOH
HOH
2005
A
HOH
2006
5
HOH
HOH
2006
A
HOH
2007
5
HOH
HOH
2007
A
HOH
2008
5
HOH
HOH
2008
A
HOH
2009
5
HOH
HOH
2009
A
HOH
2010
5
HOH
HOH
2010
A
HOH
2011
5
HOH
HOH
2011
A
HOH
2012
5
HOH
HOH
2012
A
HOH
2013
5
HOH
HOH
2013
A
HOH
2014
5
HOH
HOH
2014
A
HOH
2015
5
HOH
HOH
2015
A
HOH
2016
5
HOH
HOH
2016
A
HOH
2001
5
HOH
HOH
2001
B
HOH
2002
5
HOH
HOH
2002
B
HOH
2003
5
HOH
HOH
2003
B
HOH
2004
5
HOH
HOH
2004
B
HOH
2005
5
HOH
HOH
2005
B
HOH
2006
5
HOH
HOH
2006
B
HOH
2007
5
HOH
HOH
2007
B
HOH
2008
5
HOH
HOH
2008
B
HOH
2009
5
HOH
HOH
2009
B
HOH
2010
5
HOH
HOH
2010
B
HOH
2011
5
HOH
HOH
2011
B
HOH
2012
5
HOH
HOH
2012
B
HOH
2013
5
HOH
HOH
2013
B
HOH
2014
5
HOH
HOH
2014
B
HOH
2015
5
HOH
HOH
2015
B
HOH
2016
5
HOH
HOH
2016
B
HOH
2017
5
HOH
HOH
2017
B
HOH
2018
5
HOH
HOH
2018
B
HOH
2019
5
HOH
HOH
2019
B
HOH
2020
5
HOH
HOH
2020
B
HOH
2021
5
HOH
HOH
2021
B
HOH
2022
5
HOH
HOH
2022
B
HOH
2023
5
HOH
HOH
2023
B
HOH
2024
5
HOH
HOH
2024
B
HOH
2025
5
HOH
HOH
2025
B
HOH
2026
5
HOH
HOH
2026
B
HOH
2027
5
HOH
HOH
2027
B
HOH
3004
5
HOH
HOH
3004
B
HOH
2001
5
HOH
HOH
2001
C
HOH
2002
5
HOH
HOH
2002
C
HOH
2003
5
HOH
HOH
2003
C
HOH
2004
5
HOH
HOH
2004
C
HOH
2005
5
HOH
HOH
2005
C
HOH
2006
5
HOH
HOH
2006
C
HOH
2007
5
HOH
HOH
2007
C
HOH
2008
5
HOH
HOH
2008
C
HOH
2009
5
HOH
HOH
2009
C
HOH
2010
5
HOH
HOH
2010
C
HOH
2011
5
HOH
HOH
2011
C
HOH
2012
5
HOH
HOH
2012
C
HOH
2013
5
HOH
HOH
2013
C
HOH
2014
5
HOH
HOH
2014
C
HOH
2015
5
HOH
HOH
2015
C
HOH
2016
5
HOH
HOH
2016
C
HOH
2017
5
HOH
HOH
2017
C
HOH
2018
5
HOH
HOH
2018
C
HOH
2001
5
HOH
HOH
2001
D
HOH
2002
5
HOH
HOH
2002
D
HOH
2003
5
HOH
HOH
2003
D
HOH
2004
5
HOH
HOH
2004
D
HOH
2005
5
HOH
HOH
2005
D
HOH
2006
5
HOH
HOH
2006
D
HOH
2007
5
HOH
HOH
2007
D
HOH
2008
5
HOH
HOH
2008
D
HOH
2009
5
HOH
HOH
2009
D
HOH
2010
5
HOH
HOH
2010
D
HOH
2011
5
HOH
HOH
2011
D
MLU
1
n
1
MLU
1
A
OMZ
2
n
2
OMZ
2
A
ASN
3
n
3
ASN
3
A
GHP
4
n
4
GHP
4
A
GHP
5
n
5
GHP
5
A
OMX
6
n
6
OMX
6
A
3FG
7
n
7
3FG
7
A
MLU
1
n
1
MLU
1
B
OMZ
2
n
2
OMZ
2
B
ASN
3
n
3
ASN
3
B
GHP
4
n
4
GHP
4
B
GHP
5
n
5
GHP
5
B
OMX
6
n
6
OMX
6
B
3FG
7
n
7
3FG
7
B
MLU
1
n
1
MLU
1
C
OMZ
2
n
2
OMZ
2
C
ASN
3
n
3
ASN
3
C
GHP
4
n
4
GHP
4
C
GHP
5
n
5
GHP
5
C
OMX
6
n
6
OMX
6
C
3FG
7
n
7
3FG
7
C
MLU
1
n
1
MLU
1
D
OMZ
2
n
2
OMZ
2
D
ASN
3
n
3
ASN
3
D
GHP
4
n
4
GHP
4
D
GHP
5
n
5
GHP
5
D
OMX
6
n
6
OMX
6
D
3FG
7
n
7
3FG
7
D
0.2075
0.2197
0.2043
0.2155
0.2467
0.2651
394
449
5.2
5.1
7718
author_and_software_defined_assembly
PISA
2
dimeric
author_and_software_defined_assembly
PISA
2
dimeric
A
OMX
6
(BETAR)-BETA-HYDROXY-L-TYROSINE
A
OMX
6
TYR
B
OMX
6
(BETAR)-BETA-HYDROXY-L-TYROSINE
B
OMX
6
TYR
C
OMX
6
(BETAR)-BETA-HYDROXY-L-TYROSINE
C
OMX
6
TYR
D
OMX
6
(BETAR)-BETA-HYDROXY-L-TYROSINE
D
OMX
6
TYR
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
B
HOH
2009
P
HOH
1
B
HOH
2026
P
HOH
1
D
HOH
2003
R
HOH
1
A
ASN
3
-104.45
-64.65
0.2651
0.2197
0.2155
1.90
23.23
2176
449
8592
1843
5.1
99.5
SHELLS
1
THROUGHOUT
0.0
MAD
ENGH AND HUBER
MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
9
432.90
521.80
1.90
23.23
73
525
136
0
316
0.013
0.048
0.051
0.030
0.009
0.038
1.900
23.230
1HHA
8592
0.03820
1
26.2000
10.500
99.5
0.10310
1.90
2.00
7.280
1
10.70
99.8
data reduction
DENZO
data scaling
SCALEPACK
phasing
SHELX
phasing
DM
refinement
SHELXL-97
DECAPLANIN
Decaplanin first P6122-Form
1
N
N
1
N
N
1
N
N
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
3
N
N
4
N
N
3
N
N
3
N
N
4
N
N
5
N
N
5
N
N
5
N
N
5
N
N
covale
1.340
both
A
MLU
1
A
C
MLU
1
1_555
A
OMZ
2
A
N
OMZ
2
1_555
covale
1.351
both
A
OMZ
2
A
C
OMZ
2
1_555
A
ASN
3
A
N
ASN
3
1_555
covale
1.406
none
A
OMZ
2
A
OH
OMZ
2
1_555
A
GHP
4
A
C5
GHP
4
1_555
covale
1.340
both
A
ASN
3
A
C
ASN
3
1_555
A
GHP
4
A
N
GHP
4
1_555
covale
1.375
both
A
GHP
4
A
C
GHP
4
1_555
A
GHP
5
A
N
GHP
5
1_555
covale
1.411
none
A
GHP
4
A
C3
GHP
4
1_555
A
OMX
6
A
OH
OMX
6
1_555
covale
1.425
one
A
GHP
4
A
O4
GHP
4
1_555
E
BGC
1
E
C1
BGC
1_555
covale
1.336
both
A
GHP
5
A
C
GHP
5
1_555
A
OMX
6
A
N
OMX
6
1_555
covale
1.508
none
A
GHP
5
A
C3
GHP
5
1_555
A
3FG
7
A
CG1
3FG
7
1_555
covale
1.369
both
A
OMX
6
A
C
OMX
6
1_555
A
3FG
7
A
N
3FG
7
1_555
covale
1.403
one
A
OMX
6
A
OC
OMX
6
1_555
A
ERE
8
I
C1
ERE
1_555
covale
1.338
both
B
MLU
1
B
C
MLU
1
1_555
B
OMZ
2
B
N
OMZ
2
1_555
covale
1.349
both
B
OMZ
2
B
C
OMZ
2
1_555
B
ASN
3
B
N
ASN
3
1_555
covale
1.410
none
B
OMZ
2
B
OH
OMZ
2
1_555
B
GHP
4
B
C5
GHP
4
1_555
covale
1.339
both
B
ASN
3
B
C
ASN
3
1_555
B
GHP
4
B
N
GHP
4
1_555
covale
1.379
both
B
GHP
4
B
C
GHP
4
1_555
B
GHP
5
B
N
GHP
5
1_555
covale
1.413
none
B
GHP
4
B
C3
GHP
4
1_555
B
OMX
6
B
OH
OMX
6
1_555
covale
1.423
one
B
GHP
4
B
O4
GHP
4
1_555
F
BGC
1
F
C1
BGC
1_555
covale
1.333
both
B
GHP
5
B
C
GHP
5
1_555
B
OMX
6
B
N
OMX
6
1_555
covale
1.507
none
B
GHP
5
B
C3
GHP
5
1_555
B
3FG
7
B
CG1
3FG
7
1_555
covale
1.370
both
B
OMX
6
B
C
OMX
6
1_555
B
3FG
7
B
N
3FG
7
1_555
covale
1.402
one
B
OMX
6
B
OC
OMX
6
1_555
B
ERE
8
J
C1
ERE
1_555
covale
1.336
both
C
MLU
1
C
C
MLU
1
1_555
C
OMZ
2
C
N
OMZ
2
1_555
covale
1.350
both
C
OMZ
2
C
C
OMZ
2
1_555
C
ASN
3
C
N
ASN
3
1_555
covale
1.412
none
C
OMZ
2
C
OH
OMZ
2
1_555
C
GHP
4
C
C5
GHP
4
1_555
covale
1.340
both
C
ASN
3
C
C
ASN
3
1_555
C
GHP
4
C
N
GHP
4
1_555
covale
1.382
both
C
GHP
4
C
C
GHP
4
1_555
C
GHP
5
C
N
GHP
5
1_555
covale
1.415
none
C
GHP
4
C
C3
GHP
4
1_555
C
OMX
6
C
OH
OMX
6
1_555
covale
1.421
one
C
GHP
4
C
O4
GHP
4
1_555
G
BGC
1
G
C1
BGC
1_555
covale
1.336
both
C
GHP
5
C
C
GHP
5
1_555
C
OMX
6
C
N
OMX
6
1_555
covale
1.504
none
C
GHP
5
C
C3
GHP
5
1_555
C
3FG
7
C
CG1
3FG
7
1_555
covale
1.370
both
C
OMX
6
C
C
OMX
6
1_555
C
3FG
7
C
N
3FG
7
1_555
covale
1.402
one
C
OMX
6
C
OC
OMX
6
1_555
C
ERE
8
L
C1
ERE
1_555
covale
1.339
both
D
MLU
1
D
C
MLU
1
1_555
D
OMZ
2
D
N
OMZ
2
1_555
covale
1.353
both
D
OMZ
2
D
C
OMZ
2
1_555
D
ASN
3
D
N
ASN
3
1_555
covale
1.411
none
D
OMZ
2
D
OH
OMZ
2
1_555
D
GHP
4
D
C5
GHP
4
1_555
covale
1.338
both
D
ASN
3
D
C
ASN
3
1_555
D
GHP
4
D
N
GHP
4
1_555
covale
1.372
both
D
GHP
4
D
C
GHP
4
1_555
D
GHP
5
D
N
GHP
5
1_555
covale
1.415
none
D
GHP
4
D
C3
GHP
4
1_555
D
OMX
6
D
OH
OMX
6
1_555
covale
1.423
one
D
GHP
4
D
O4
GHP
4
1_555
H
BGC
1
H
C1
BGC
1_555
covale
1.333
both
D
GHP
5
D
C
GHP
5
1_555
D
OMX
6
D
N
OMX
6
1_555
covale
1.505
none
D
GHP
5
D
C3
GHP
5
1_555
D
3FG
7
D
CG1
3FG
7
1_555
covale
1.372
both
D
OMX
6
D
C
OMX
6
1_555
D
3FG
7
D
N
3FG
7
1_555
covale
1.405
one
D
OMX
6
D
OC
OMX
6
1_555
D
ERE
8
M
C1
ERE
1_555
covale
1.415
one
E
BGC
1
E
O2
BGC
1_555
E
RAM
2
E
C1
RAM
1_555
covale
1.417
one
F
BGC
1
F
O2
BGC
1_555
F
RAM
2
F
C1
RAM
1_555
covale
1.413
one
G
BGC
1
G
O2
BGC
1_555
G
RAM
2
G
C1
RAM
1_555
covale
1.423
one
H
BGC
1
H
O2
BGC
1_555
H
RAM
2
H
C1
RAM
1_555
ANTIBIOTIC
ANTIBIOTIC, GLYCOPEPTIDE
A
GHP
5
A
GHP
5
1
A
OMX
6
A
OMX
6
2.21
B
GHP
5
B
GHP
5
1
B
OMX
6
B
OMX
6
13.74
C
GHP
5
C
GHP
5
1
C
OMX
6
C
OMX
6
8.58
D
GHP
5
D
GHP
5
1
D
OMX
6
D
OMX
6
10.07
given
-0.709590
0.350320
-0.611360
0.381210
-0.538840
-0.751220
-0.592600
-0.766110
0.248810
-26.04679
47.57551
15.97865
given
-0.709590
0.350320
-0.611360
0.381210
-0.538840
-0.751220
-0.592600
-0.766110
0.248810
-26.04679
47.57551
15.97865
given
-0.324140
-0.596990
-0.733850
-0.860890
0.507740
-0.032800
0.392190
0.621130
-0.678520
20.79205
9.15937
-7.92575
NOR00692
NOR
1
NOR00692
1
7
1HHA
1
7
NOR00692
A
1
1
7
1
7
1HHA
1
7
NOR00692
B
1
1
7
1
7
1HHA
1
7
NOR00692
C
1
1
7
1
7
1HHA
1
7
NOR00692
D
1
1
7
178
P 61 2 2