1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Hsu, S.-T.D.
Breukink, E.
Tischenko, E.
Lutters, M.A.G.
de Kruijff, B.
Kaptein, R.
Bonvin, A.M.J.J.
van Nuland, N.A.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C3 H7 N O2
89.093
D-ALANINE
D-peptide linking
C4 H9 N O2
103.120
D-ALPHA-AMINOBUTYRIC ACID
D-peptide linking
C4 H7 N O2
101.104
n
(2Z)-2-AMINOBUT-2-ENOIC ACID
Z-DEHYDROBUTYRINE
peptide linking
C3 H5 N O2
87.077
n
2-AMINO-ACRYLIC ACID
2,3-DIDEHYDROALANINE
peptide linking
C15 H26 F2 O7 P2
418.307
(2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate
non-polymer
C5 H9 N O4
147.129
GAMMA-D-GLUTAMIC ACID
D-GLUTAMIC ACID
D-gamma-peptide, C-delta linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C11 H19 N O8
293.270
N-acetyl-alpha-muramic acid
D-saccharide, alpha linking
C8 H15 N O6
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
D-saccharide, beta linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
Nat. Struct. Mol. Biol.
1545-9993
11
963
967
10.1038/nsmb830
15361862
The nisin-lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics.
2004
US
Biochemistry
BICHAW
0033
0006-2960
41
7670
10.1021/BI025679T
12056898
Mapping the Targeted Membrane Pore Formation Mechanism by Solution NMR: The Nisin Z and Lipid II Interaction in Sds Micelles
2002
US
Science
SCIEAS
0038
0036-8075
286
2361
10.1126/SCIENCE.286.5448.2361
10600751
Use of the Cell Wall Precursor Lipid II by a Pore- Forming Peptide Antibiotic
1999
US
Proteins: Struct.,Funct., Genet.
PSFGEY
0867
0887-3585
50
496
10.1002/PROT.10299
12557191
Refinement of Protein Structures in Explicit Solvent
2003
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
125
1731
10.1021/JA026939X
12580598
Haddock: A Protein-Protein Docking Approach Based on Biochemical or Biophysical Information
2003
MUB A 1 HAS WRONG CHIRALITY AT ATOM C9
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
489.542
ALA-FGA-LYS-DAL-DAL PEPTIDE
1
nat
polymer
3345.146
Lantibiotic
1
nat
polymer
496.463
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid
1
man
branched
418.307
(2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate
1
syn
non-polymer
no
yes
A(FGA)K(DAL)(DAL)
AEKAA
L
polypeptide(L)
no
yes
I(DBU)(DAL)I(DHA)LC(DBB)PGCK(DBB)GALMGCNMK(DBB)A(DBB)CNCSIHV(DHA)K
ITAISLCTPGCKTGALMGCNMKTATCNCSIHVSK
N
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
sample
1
5
71816
MONARTHROPALPUS FLAVUS
sample
1
34
1358
Lactococcus lactis
atom_site
citation
citation_author
database_PDB_caveat
pdbx_nmr_spectrometer
pdbx_validate_polymer_linkage
atom_site
chem_comp
database_PDB_caveat
entity
entity_poly
entity_poly_seq
entity_src_nat
pdbx_database_status
pdbx_entity_nonpoly
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_nonpoly_scheme
pdbx_poly_seq_scheme
pdbx_struct_assembly_gen
pdbx_struct_assembly_prop
pdbx_struct_mod_residue
pdbx_struct_oper_list
pdbx_unobs_or_zero_occ_atoms
pdbx_validate_chiral
pdbx_validate_close_contact
struct_asym
struct_conn
struct_ref
struct_ref_seq
struct_ref_seq_dif
struct_site_gen
atom_site
chem_comp
database_PDB_caveat
entity
pdbx_branch_scheme
pdbx_chem_comp_identifier
pdbx_entity_branch
pdbx_entity_branch_descriptor
pdbx_entity_branch_link
pdbx_entity_branch_list
pdbx_entity_nonpoly
pdbx_nonpoly_scheme
pdbx_struct_assembly_gen
pdbx_unobs_or_zero_occ_atoms
pdbx_validate_chiral
pdbx_validate_close_contact
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
Advisory
Atomic model
Data collection
Database references
Advisory
Atomic model
Data collection
Database references
Derived calculations
Non-polymer description
Other
Polymer sequence
Source and taxonomy
Structure summary
Advisory
Atomic model
Data collection
Derived calculations
Structure summary
1
0
2005-03-07
1
1
2011-07-13
1
2
2012-11-30
2
0
2018-01-17
3
0
2020-07-08
4
0
2020-07-29
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_atom_id
_atom_site.label_atom_id
_citation.journal_abbrev
_citation.page_last
_citation.pdbx_database_id_DOI
_citation.title
_citation_author.name
_pdbx_nmr_spectrometer.manufacturer
_pdbx_nmr_spectrometer.model
_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.group_PDB
_atom_site.label_asym_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.type_symbol
_chem_comp.formula
_chem_comp.formula_weight
_chem_comp.id
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.type
_database_PDB_caveat.text
_entity_poly.pdbx_seq_one_letter_code
_entity_poly.pdbx_seq_one_letter_code_can
_entity_src_nat.pdbx_beg_seq_num
_entity_src_nat.pdbx_end_seq_num
_entity_src_nat.pdbx_organism_scientific
_entity_src_nat.strain
_pdbx_database_status.status_code_mr
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_prop.value
_pdbx_struct_mod_residue.details
_pdbx_struct_oper_list.symmetry_operation
_pdbx_validate_chiral.auth_seq_id
_pdbx_validate_close_contact.auth_asym_id_2
_pdbx_validate_close_contact.auth_atom_id_1
_pdbx_validate_close_contact.auth_atom_id_2
_pdbx_validate_close_contact.auth_comp_id_1
_pdbx_validate_close_contact.auth_comp_id_2
_pdbx_validate_close_contact.auth_seq_id_1
_pdbx_validate_close_contact.auth_seq_id_2
_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_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_seq_id
_struct_ref.db_code
_struct_ref.pdbx_align_begin
_struct_ref.pdbx_db_accession
_struct_ref.pdbx_seq_one_letter_code
_struct_ref_seq.db_align_beg
_struct_ref_seq.pdbx_auth_seq_align_beg
_struct_ref_seq.pdbx_db_accession
_struct_ref_seq.seq_align_end
_struct_site_gen.auth_asym_id
_struct_site_gen.auth_comp_id
_struct_site_gen.auth_seq_id
_struct_site_gen.label_asym_id
_struct_site_gen.label_comp_id
_struct_site_gen.label_seq_id
_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_asym_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_entity_id
_atom_site.type_symbol
_chem_comp.name
_database_PDB_caveat.text
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_unobs_or_zero_occ_atoms.label_asym_id
_pdbx_validate_chiral.auth_asym_id
_pdbx_validate_chiral.auth_seq_id
_pdbx_validate_close_contact.auth_asym_id_1
_pdbx_validate_close_contact.auth_asym_id_2
_pdbx_validate_close_contact.auth_atom_id_1
_pdbx_validate_close_contact.auth_atom_id_2
_pdbx_validate_close_contact.auth_comp_id_1
_pdbx_validate_close_contact.auth_comp_id_2
_pdbx_validate_close_contact.auth_seq_id_1
_pdbx_validate_close_contact.auth_seq_id_2
_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
L
MUB
2
n
A
MUB
1
L
NAG
1
n
A
NAG
2
a-D-GlcpNAc3<C3O2>
MurNAc
DGlcpNAcb
N-acetyl-b-D-glucopyranosamine
b-D-GlcpNAc
GlcNAc
2005-03-07
SPRSDE
SOLUTION STRUCTURE OF THE LANTIBIOTIC ACTAGARDINE
SOLUTION STRUCTURE OF TYPE B LANTIBIOTICS MERSACIDIN IN MEOH/H2O MIXTURE
SOLUTION STRUCTURE OF TYPE B LANTIBIOTICS MERSACIDIN IN DPC MICELLES
SOLUTION STRUCTURE OF TYPE B LANTIBIOTICS MERSACIDIN BOUND TO LIPID II IN DPC MICELLES
CRYSTAL STRUCTURE OF THE TUPE B LANTIBIOTIC MERSACIDIN
SOLUTION STRUCTURE OF THE LANTIBIOTIC EPILANCIN 15X
SOLUTION STRUCTURE OF THE LANTIBIOTIC CINNAMYCIN COMPLEXED WITH LYSOPHOSPHATIDYLETHANOLAMINE
SOLUTION STRUCTURE OF LCH-ALPHA PEPTIDE FROM TWO-COMPONENT LANTIBIOTIC SYSTEM LICHENICIDIN VK21 A1
SOLUTION STRUCTURE OF LCH-BETA PEPTIDE FROM TWO-COMPONENT LANTIBIOTIC LICHENICIDIN VK21 A2
PDBE
Y
PDBE
2004-11-19
REL
REL
oligosaccharide
DGlcpNAcb1-4MurNAc1-ROH
3
GMML
1.0
Glycam Condensed Sequence
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O_3*OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1
3
PDB2Glycan
1.1.0
WURCS
[][a-D-GlcpNAc]{[(3+1)][<C3O1>]{}[(4+1)][b-D-GlcpNAc]{}}
3
PDB-CARE
LINUCS
C1
O4
NAG
MUB
2
1
3
O1
HO4
sing
n
n
FDF
(2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate
NISIN Z IS A LANTIBIOTIC. THE LANTIBIOTICS
ARE CHARACTERIZED BY LANTHIONINE AND/OR METHYLLANTHIONINE
NONPROTEINOGENIC AMINO ACIDS.
HERE, NISIN Z IS REPRESENTED BY THE SEQUENCE (SEQRES)
GROUP: 1
NAME: NISIN Z
CHAIN: N
COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 34
DESCRIPTION: NISIN Z IS A PENTACYCLIC PEPTIDE. THIOETHER BONDS
WITH CYSTEINE RESULT IN FIVE CYCLIC STRUCTURES ALONG
THE PEPTIDE CHAIN.
CROSSLINK 3-7 METHYLLANTHIONINE (DAL-CYS)
CROSSLINK 8-11 BETA-METHYLLANTHIONINE (DBB-CYS)
CROSSLINK 13-19 BETA-METHYLLANTHIONINE (DBB-CYS)
CROSSLINK 23-26 BETA-METHYLLANTHIONINE (DBB-CYS)
CROSSLINK 25-28 BETA-METHYLLANTHIONINE (DBB-CYS)
Lantibiotic
Nisin Z is a heptacyclic peptide. Post Translational maturation of
lantibiotics involves the enzymic conversion of Thr, and Ser into
dehydrated AA and the formation of thioether bonds with cysteine.
Thioether bonds with cysteine result in five cyclic structures along
the peptide chain. This is followed by membrane translocation and
cleavage of the modified precursor.
Nisin A
Polypeptide
THE STRUCTURE WAS DETERMINED USING MULTIDIMENSIONAL NMR SPECTROSCOPY ON 15N-LABELLED NISIN IN COMPLEX WITH UNLABELLED 3-LIPID II. INTERMOLECULAR HYDROGEN BONDS WERE IDENTIFIED AND USED IN STRUCTURAL CALCULATION BY 31P- EDITED 1H-15N CT HSQC.
RMSD CLUSTERING AND LOWEST TOTAL ENERGY
200
20
1H-15N CT HSQC
31P 1D
1H-13C HSQC
1H-13C HMBC
31P 1D
1H-15N-NOESY HSQC
1H-1H NOESY
1H-15N TOCSY- HSQC
1H-1H TOCSY
1H-1H COSY
1H-15N-NOESY HSQC
1H-1H NOESY
1.0
atm
300.0
K
REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THE ENSEMBLE OF STRUCTURES IS SUPERIMPOSED ON THE CA OF NISIN RESIDUES 1-12 (CHAIN N), THE HEAVY ATOMS OF MURNAC, PYROPHOSPHATE AND THE FIRST ISOPRENE OF 3-LIPID II (CHAIN L) AS THESE ARE THE ONLY SEGMENTS THAT HAVE SUFFICIENT DISTANCE RESTRAINTS TO DEFINE THE COMPLEX STRUCTURE. OTHER RESIDUES NAMELY RESIDUES 13-34 (ESPECIALLY RESIDUES 20-34) OF NISIN, THE PENTAPEPTIDE AND TERMINAL ISOPRENE UNITS OF 3-LIPID II ARE FLEXIBLE AS SUPPORTED BY DYNAMICS DATA. THE ATOM OCCUPANCY OF THE C- TERMINAL TAIL OF NISIN (RESIDUES 20-34) HAS BEEN MODIFIED TO BE 0.3 TO REFLECT THEIR DISORDER/FLEXIBILITY.
HADDOCK
100% D6-DMSO
BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARREN
refinement
CNS
1.1
structure solution
NMRView
VIEW
structure solution
CNS
500
Bruker
AVANCE
600
Bruker
AVANCE
750
Bruker
AVANCE
900
Bruker
AVANCE
FPP
35
4
FDF
FDF
101
L
ALA
3
n
1
ALA
3
L
FGA
4
n
2
FGA
4
L
LYS
5
n
3
LYS
5
L
DAL
6
n
4
DAL
6
L
DAL
7
n
5
DAL
7
L
ILE
1
n
1
ILE
1
N
DBU
2
n
2
DBU
2
N
DAL
3
n
3
DAL
3
N
ILE
4
n
4
ILE
4
N
DHA
5
n
5
DHA
5
N
LEU
6
n
6
LEU
6
N
CYS
7
n
7
CYS
7
N
DBB
8
n
8
DBB
8
N
PRO
9
n
9
PRO
9
N
GLY
10
n
10
GLY
10
N
CYS
11
n
11
CYS
11
N
LYS
12
n
12
LYS
12
N
DBB
13
n
13
DBB
13
N
GLY
14
n
14
GLY
14
N
ALA
15
n
15
ALA
15
N
LEU
16
n
16
LEU
16
N
MET
17
n
17
MET
17
N
GLY
18
n
18
GLY
18
N
CYS
19
n
19
CYS
19
N
ASN
20
n
20
ASN
20
N
MET
21
n
21
MET
21
N
LYS
22
n
22
LYS
22
N
DBB
23
n
23
DBB
23
N
ALA
24
n
24
ALA
24
N
DBB
25
n
25
DBB
25
N
CYS
26
n
26
CYS
26
N
ASN
27
n
27
ASN
27
N
CYS
28
n
28
CYS
28
N
SER
29
n
29
SER
29
N
ILE
30
n
30
ILE
30
N
HIS
31
n
31
HIS
31
N
VAL
32
n
32
VAL
32
N
DHA
33
n
33
DHA
33
N
LYS
34
n
34
LYS
34
N
author_and_software_defined_assembly
PISA
2
dimeric
1610
3
3620
N
DBU
2
modified residue
B
DBU
2
THR
N
DHA
5
modified residue
B
DHA
5
SER
N
DHA
33
modified residue
B
DHA
33
SER
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
1
L
F1
FDF
101
D
F1
FDF
1
1
N
1
L
F2
FDF
101
D
F2
FDF
1
1
N
2
L
F1
FDF
101
D
F1
FDF
1
1
N
2
L
F2
FDF
101
D
F2
FDF
1
1
N
3
L
F1
FDF
101
D
F1
FDF
1
1
N
3
L
F2
FDF
101
D
F2
FDF
1
1
N
4
L
F1
FDF
101
D
F1
FDF
1
1
N
4
L
F2
FDF
101
D
F2
FDF
1
1
N
5
L
F1
FDF
101
D
F1
FDF
1
1
N
5
L
F2
FDF
101
D
F2
FDF
1
1
N
6
L
F1
FDF
101
D
F1
FDF
1
1
N
6
L
F2
FDF
101
D
F2
FDF
1
1
N
7
L
F1
FDF
101
D
F1
FDF
1
1
N
7
L
F2
FDF
101
D
F2
FDF
1
1
N
8
L
F1
FDF
101
D
F1
FDF
1
1
N
8
L
F2
FDF
101
D
F2
FDF
1
1
N
9
L
F1
FDF
101
D
F1
FDF
1
1
N
9
L
F2
FDF
101
D
F2
FDF
1
1
N
10
L
F1
FDF
101
D
F1
FDF
1
1
N
10
L
F2
FDF
101
D
F2
FDF
1
1
N
11
L
F1
FDF
101
D
F1
FDF
1
1
N
11
L
F2
FDF
101
D
F2
FDF
1
1
N
12
L
F1
FDF
101
D
F1
FDF
1
1
N
12
L
F2
FDF
101
D
F2
FDF
1
1
N
13
L
F1
FDF
101
D
F1
FDF
1
1
N
13
L
F2
FDF
101
D
F2
FDF
1
1
N
14
L
F1
FDF
101
D
F1
FDF
1
1
N
14
L
F2
FDF
101
D
F2
FDF
1
1
N
15
L
F1
FDF
101
D
F1
FDF
1
1
N
15
L
F2
FDF
101
D
F2
FDF
1
1
N
16
L
F1
FDF
101
D
F1
FDF
1
1
N
16
L
F2
FDF
101
D
F2
FDF
1
1
N
17
L
F1
FDF
101
D
F1
FDF
1
1
N
17
L
F2
FDF
101
D
F2
FDF
1
1
N
18
L
F1
FDF
101
D
F1
FDF
1
1
N
18
L
F2
FDF
101
D
F2
FDF
1
1
N
19
L
F1
FDF
101
D
F1
FDF
1
1
N
19
L
F2
FDF
101
D
F2
FDF
1
1
N
20
L
F1
FDF
101
D
F1
FDF
1
1
N
20
L
F2
FDF
101
D
F2
FDF
1
1
N
1
A
C9
MUB
1
PLANAR
2
A
C9
MUB
1
PLANAR
4
A
C9
MUB
1
PLANAR
5
A
C9
MUB
1
PLANAR
7
A
C9
MUB
1
PLANAR
10
A
C9
MUB
1
PLANAR
11
A
C9
MUB
1
PLANAR
12
A
C9
MUB
1
PLANAR
13
A
C9
MUB
1
PLANAR
15
A
C9
MUB
1
PLANAR
16
A
C9
MUB
1
PLANAR
17
A
C9
MUB
1
PLANAR
18
A
C9
MUB
1
PLANAR
19
A
C9
MUB
1
PLANAR
20
A
C9
MUB
1
PLANAR
1
L
L
HZ3
O
LYS
DAL
5
7
1.56
3
L
A
HG2
H62
FGA
MUB
4
1
1.15
3
N
L
HB2
H5
PRO
FDF
9
101
1.33
3
N
L
HG22
O1
ILE
FDF
1
101
1.54
4
L
A
HD3
H5
LYS
MUB
5
1
1.30
4
N
N
O
H
GLY
GLY
14
18
1.60
5
N
L
HG22
O1
ILE
FDF
1
101
1.58
5
N
N
HD1
O
HIS
LYS
31
34
1.58
6
L
A
HG2
H62
FGA
MUB
4
1
1.23
9
N
L
HB2
H5
PRO
FDF
9
101
1.28
9
N
L
HG22
O1
ILE
FDF
1
101
1.52
9
N
N
O
H
GLY
GLY
14
18
1.59
10
L
L
HZ3
OXT
LYS
DAL
5
7
1.56
13
L
A
HG3
H62
FGA
MUB
4
1
1.33
14
L
A
HG2
H62
FGA
MUB
4
1
1.26
14
L
A
OXT
H61
FGA
MUB
4
1
1.56
16
N
N
HD1
O
HIS
LYS
31
34
1.59
16
L
A
OXT
HO6
FGA
MUB
4
1
1.60
17
L
A
H1
H4
ALA
MUB
3
1
0.84
18
A
A
O3
H1
MUB
NAG
1
2
1.55
19
L
A
HZ2
O4
LYS
MUB
5
1
1.58
20
L
A
HB1
H61
ALA
MUB
3
1
1.29
1
N
DBB
8
147.76
-58.97
1
N
LYS
12
-151.30
1.93
1
N
MET
17
-154.38
-46.71
1
N
CYS
19
63.18
82.90
1
N
ASN
20
-57.88
-81.18
1
N
HIS
31
-126.21
-82.45
2
L
DAL
6
-71.81
-73.98
2
N
DBB
13
-73.72
46.61
2
N
MET
17
-160.00
-33.77
2
N
CYS
19
65.39
91.33
2
N
MET
21
73.82
39.53
3
L
DAL
6
-74.60
21.26
3
N
DBB
8
150.47
-53.57
3
N
DBB
13
-73.72
46.83
3
N
MET
17
-138.14
-30.53
3
N
CYS
19
60.11
79.16
3
N
ASN
20
-68.09
-80.10
3
N
MET
21
75.27
-31.16
3
N
DBB
23
174.54
38.88
3
N
ALA
24
-117.37
74.54
3
N
ILE
30
-90.11
55.63
4
L
DAL
6
-178.22
-82.63
4
N
LEU
6
-101.79
68.85
4
N
CYS
7
-63.52
99.10
4
N
DBB
8
150.92
-57.27
4
N
DBB
13
-73.79
44.97
4
N
MET
17
-150.61
-36.02
4
N
CYS
19
70.22
87.97
4
N
MET
21
74.53
-49.92
5
L
DAL
6
145.50
40.04
5
N
DBB
8
153.14
-53.07
5
N
DBB
13
-81.60
25.69
5
N
MET
17
-149.99
-57.69
5
N
CYS
19
65.63
70.83
5
N
ASN
20
70.51
-81.51
6
L
DAL
6
-75.27
46.55
6
N
CYS
7
-59.40
90.44
6
N
DBB
8
150.13
-54.95
6
N
DBB
13
-73.93
32.70
6
N
MET
17
-152.97
-42.41
6
N
ASN
20
174.42
-23.20
6
N
ILE
30
-91.79
32.34
7
L
DAL
6
170.25
-37.64
7
N
CYS
7
-59.99
99.45
7
N
DBB
8
146.75
-53.50
7
N
DBB
13
-70.51
52.35
7
N
MET
17
-136.07
-58.47
7
N
CYS
19
64.80
177.59
7
N
ASN
20
-119.19
-71.63
7
N
MET
21
73.57
-47.13
7
N
DBB
23
155.26
33.29
8
N
DBB
13
-70.92
50.83
8
N
ALA
15
-79.02
21.81
8
N
MET
17
-172.30
-30.90
8
N
ASN
20
179.32
-22.05
8
N
MET
21
75.76
-65.11
9
N
DBB
8
150.53
-55.48
9
N
DBB
13
-76.75
28.34
9
N
MET
17
-158.99
-41.37
9
N
CYS
19
63.11
88.32
9
N
MET
21
72.13
-49.53
10
N
DBB
8
140.28
-51.06
10
N
LYS
12
-140.84
14.19
10
N
DBB
13
-72.49
53.85
10
N
MET
17
-163.81
-42.48
10
N
CYS
19
65.03
77.38
10
N
ASN
20
-68.84
-85.39
11
N
DBB
8
143.70
-49.16
11
N
DBB
13
-71.95
50.51
11
N
ALA
15
-75.07
28.20
11
N
MET
17
179.56
-26.65
11
N
DBB
23
-177.58
46.61
12
N
DBB
8
143.59
-55.55
12
N
DBB
13
-71.21
58.25
12
N
MET
17
-154.64
-49.22
12
N
CYS
19
63.45
99.75
12
N
ASN
20
-72.79
-98.27
12
N
ILE
30
-81.86
35.64
13
N
DBB
13
-76.07
35.24
13
N
ASN
20
73.71
-88.65
14
N
CYS
7
-61.82
99.58
14
N
DBB
13
-68.14
46.07
14
N
ALA
15
-75.16
29.46
14
N
MET
17
178.46
-33.69
14
N
CYS
19
75.05
-65.87
14
N
ASN
20
-173.18
-39.26
14
N
MET
21
74.54
-43.78
14
N
DBB
23
-174.89
26.50
15
L
DAL
6
148.83
-34.55
15
N
DBB
8
150.40
-58.71
15
N
DBB
13
-75.98
24.17
15
N
MET
17
-156.02
-44.07
15
N
CYS
19
75.01
-24.27
15
N
ASN
20
-172.07
-68.37
15
N
SER
29
-69.29
98.60
16
N
DBB
8
146.93
-53.89
16
N
DBB
13
-71.36
54.04
16
N
MET
17
-132.83
-66.27
16
N
ASN
20
-83.05
-97.80
16
N
DBB
23
147.54
32.18
16
N
ALA
24
-92.82
57.44
16
N
ILE
30
-86.91
49.49
17
N
DBB
13
-73.49
50.91
17
N
ALA
15
-76.73
28.51
17
N
MET
17
-174.22
-28.53
17
N
CYS
19
64.22
70.08
17
N
ASN
20
-128.41
-68.79
17
N
DBB
23
-70.61
58.28
18
L
DAL
6
171.54
-80.63
18
N
DBB
13
-73.58
52.26
18
N
ALA
15
-77.60
37.21
18
N
MET
17
175.46
-34.28
18
N
MET
21
76.41
-28.66
19
L
DAL
6
168.96
29.97
19
N
DBB
8
151.16
-52.95
19
N
DBB
13
-73.79
52.82
19
N
ALA
15
-78.18
28.35
19
N
MET
17
-143.10
-12.74
19
N
MET
21
70.87
-1.49
19
N
DBB
23
137.40
33.35
19
N
HIS
31
-95.08
-71.87
20
L
DAL
6
-71.59
0.68
20
N
CYS
7
-66.03
97.78
20
N
DBB
8
145.18
-50.86
20
N
DBB
13
-71.67
52.44
20
N
ALA
15
-78.86
29.70
20
N
MET
17
-174.47
-46.32
20
N
CYS
19
65.31
62.64
20
N
ASN
20
70.42
-57.45
NAG-MUB-ALA-FGA-LYS-DAL-DAL PEPTIDE, NISIN Z
The solution structure of the nisin-lipid II complex
1
N
N
2
N
N
3
N
N
4
N
N
N
DBB
8
B
DBB
8
HELX_P
N
DBB
13
B
DBB
13
1
1
6
covale
1.318
both
L
ALA
3
A
C
ALA
1
1_555
L
FGA
4
A
N
FGA
2
1_555
covale
1.326
one
L
ALA
3
A
N
ALA
1
1_555
A
MUB
1
C
C10
MUB
1_555
covale
1.322
both
L
FGA
4
A
CD
FGA
2
1_555
L
LYS
5
A
N
LYS
3
1_555
covale
1.334
both
L
LYS
5
A
C
LYS
3
1_555
L
DAL
6
A
N
DAL
4
1_555
covale
1.337
both
L
DAL
6
A
C
DAL
4
1_555
L
DAL
7
A
N
DAL
5
1_555
covale
1.605
one
L
FDF
101
D
PB
FDF
1_555
A
MUB
1
C
O1
MUB
1_555
covale
1.341
both
N
ILE
1
B
C
ILE
1
1_555
N
DBU
2
B
N
DBU
2
1_555
covale
1.319
both
N
DBU
2
B
C
DBU
2
1_555
N
DAL
3
B
N
DAL
3
1_555
covale
1.318
both
N
DAL
3
B
C
DAL
3
1_555
N
ILE
4
B
N
ILE
4
1_555
covale
1.794
none
N
DAL
3
B
CB
DAL
3
1_555
N
CYS
7
B
SG
CYS
7
1_555
covale
1.336
both
N
ILE
4
B
C
ILE
4
1_555
N
DHA
5
B
N
DHA
5
1_555
covale
1.321
both
N
DHA
5
B
C
DHA
5
1_555
N
LEU
6
B
N
LEU
6
1_555
covale
1.319
one
N
CYS
7
B
C
CYS
7
1_555
N
DBB
8
B
N
DBB
8
1_555
covale
1.346
both
N
DBB
8
B
C
DBB
8
1_555
N
PRO
9
B
N
PRO
9
1_555
covale
1.815
none
N
DBB
8
B
CB
DBB
8
1_555
N
CYS
11
B
SG
CYS
11
1_555
covale
1.326
one
N
LYS
12
B
C
LYS
12
1_555
N
DBB
13
B
N
DBB
13
1_555
covale
1.328
both
N
DBB
13
B
C
DBB
13
1_555
N
GLY
14
B
N
GLY
14
1_555
covale
1.828
none
N
DBB
13
B
CB
DBB
13
1_555
N
CYS
19
B
SG
CYS
19
1_555
covale
1.321
one
N
LYS
22
B
C
LYS
22
1_555
N
DBB
23
B
N
DBB
23
1_555
covale
1.328
both
N
DBB
23
B
C
DBB
23
1_555
N
ALA
24
B
N
ALA
24
1_555
covale
1.823
none
N
DBB
23
B
CB
DBB
23
1_555
N
CYS
26
B
SG
CYS
26
1_555
covale
1.323
one
N
ALA
24
B
C
ALA
24
1_555
N
DBB
25
B
N
DBB
25
1_555
covale
1.323
both
N
DBB
25
B
C
DBB
25
1_555
N
CYS
26
B
N
CYS
26
1_555
covale
1.817
none
N
DBB
25
B
CB
DBB
25
1_555
N
CYS
28
B
SG
CYS
28
1_555
covale
1.326
both
N
VAL
32
B
C
VAL
32
1_555
N
DHA
33
B
N
DHA
33
1_555
covale
1.324
both
N
DHA
33
B
C
DHA
33
1_555
N
LYS
34
B
N
LYS
34
1_555
covale
1.424
both
A
MUB
1
C
O4
MUB
1_555
A
NAG
2
C
C1
NAG
1_555
PEPTIDE/ANTIBIOTIC
PEPTIDE-ANTIBIOTIC COMPLEX, LANTIBIOTIC, ANTIMICROBIAL, BACTERIOCIN, THIOESTER, PORE FORMATION, PYROPHOSPHATE CAGE, FOOD PRESERVATIVE
1WCO
PDB
1
1
1WCO
Q7BB86_9LACT
UNP
2
24
Q7BB86
ITSISLCTPGCKTGALMGCNMKTATCNCSIHVSK
3
7
1WCO
3
7
1WCO
L
1
1
5
24
57
1WCO
1
34
Q7BB86
N
2
1
34
2
SER
conflict
DAL
3
1WCO
N
Q7BB86
UNP
26
3
2
THR
conflict
DBB
8
1WCO
N
Q7BB86
UNP
31
8
2
THR
conflict
DBB
13
1WCO
N
Q7BB86
UNP
36
13
2
THR
conflict
DBB
23
1WCO
N
Q7BB86
UNP
46
23
2
THR
conflict
DBB
25
1WCO
N
Q7BB86
UNP
48
25
1
P 1