1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Phan Chan Du, A.
Limal, D.
Semetey, V.
Dali, H.
Jolivet, M.
Desgranges, C.
Cung, M.T.
Briand, J.P.
Petit, M.C.
Muller, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C2 H4 O
44.053
ACETYL GROUP
non-polymer
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C3 H8 N2 O2
104.108
n
DIAMINOPROPANOIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
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
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
323
503
521
10.1016/S0022-2836(02)00701-5
12381305
Structural and immunological characterisation of heteroclitic peptide analogues corresponding to the 600-612 region of the HIV envelope gp41 glycoprotein.
2002
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1373.556
Transmembrane protein gp41
1
syn
polymer
TM, Glycoprotein 41, gp41
no
yes
(ACE)IWG(DPP)SGKLIDTTA
XIWGASGKLIDTTA
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
database_PDB_caveat
pdbx_struct_assembly
pdbx_struct_assembly_prop
pdbx_struct_oper_list
pdbx_validate_polymer_linkage
atom_site
cell
chem_comp
database_PDB_caveat
diffrn
diffrn_radiation
diffrn_radiation_wavelength
entity
entity_name_com
entity_poly
entity_poly_seq
pdbx_entity_src_syn
pdbx_nmr_details
pdbx_nmr_exptl_sample_conditions
pdbx_nmr_refine
pdbx_nmr_sample_details
pdbx_nmr_software
pdbx_poly_seq_scheme
pdbx_struct_mod_residue
pdbx_unobs_or_zero_occ_atoms
pdbx_validate_chiral
pdbx_validate_close_contact
pdbx_validate_torsion
struct
struct_conn
struct_ref
struct_ref_seq
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Advisory
Data collection
Derived calculations
Advisory
Atomic model
Data collection
Database references
Derived calculations
Experimental preparation
Non-polymer description
Other
Polymer sequence
Refinement description
Source and taxonomy
Structure summary
1
0
2003-07-01
1
1
2008-04-27
1
2
2011-07-13
1
3
2018-10-03
2
0
2018-10-10
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.type_symbol
_chem_comp.formula
_chem_comp.formula_weight
_chem_comp.id
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.type
_entity.formula_weight
_entity.pdbx_description
_entity_poly.pdbx_seq_one_letter_code
_entity_poly.pdbx_seq_one_letter_code_can
_entity_poly_seq.mon_id
_pdbx_entity_src_syn.ncbi_taxonomy_id
_pdbx_entity_src_syn.organism_scientific
_pdbx_entity_src_syn.pdbx_beg_seq_num
_pdbx_entity_src_syn.pdbx_end_seq_num
_pdbx_nmr_details.text
_pdbx_nmr_exptl_sample_conditions.pressure
_pdbx_nmr_exptl_sample_conditions.pressure_units
_pdbx_nmr_refine.method
_pdbx_nmr_refine.software_ordinal
_pdbx_nmr_sample_details.contents
_pdbx_nmr_software.authors
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.pdb_mon_id
_pdbx_struct_mod_residue.auth_comp_id
_pdbx_struct_mod_residue.label_comp_id
_struct.pdbx_descriptor
_struct.title
_struct_ref.db_code
_struct_ref.db_name
_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.db_align_end
_struct_ref_seq.pdbx_auth_seq_align_beg
_struct_ref_seq.pdbx_db_accession
_struct_ref_seq.seq_align_beg
1IM7 contains the parent peptide
1J8N contains the beta3-ser analogue peptide (HSER)
1J8Z contains the beta3-Cys analogue peptide (HCYS)
1J9V contains the lactam analogue peptide DabD
1JAR contains the lactam analogue peptidev DDab
1JC8 contains the lactam analogue peptide DDap
1JAA contains the lactam analogue peptide DapE
1JCP contains the lactam analogue peptide EDap
RCSB
Y
RCSB
2001-06-13
REL
REL
The parent peptide (IWGCSGKLICTTA) occurs naturally in HIV gp41
11676
Human immunodeficiency virus 1
sample
1
14
Classical 2D homonuclear NMR technques were used. Different NOESY with different mixing time (from 80ms to 800ms) were recorded in order to determine the best conditions without spin diffusion.
structures with the lowest energy
50
20
2D NOESY
DQF-COSY
TOCSY
ambient
298
K
50 initial structures were generated using DYANA software, followed by 500 steps restrained minimization.Then using DISCOVER 3, 35 ps MD and 750 steps conjugate gradient EM.
torsion dynamics, molecular dynamics, energy minimization
1
lowest energy
4mM peptide in 500 ul solvent
100% DMSO-D6
Bruker GMBH
collection
XWINNMR
2.6
Bruker GMBH
processing
XWINNMR
2.6
Bartels C., Billeter M., Guentert P. and Wuethrich K. (1995) J.Biomol. NMR, 5, 1-10
data analysis
XEASY
1.2
Guentert P., Mumenthaler C. and Wuethrich K. (1997) J. Mol. Biol., 273,283-298
refinement
DYANA
1.5
MSI, San Diego
refinement
DISCOVER
3
400
Bruker
Avance
600
Bruker
Avance
ACE
1
n
1
ACE
1
A
ILE
2
n
2
ILE
2
A
TRP
3
n
3
TRP
3
A
GLY
4
n
4
GLY
4
A
DNP
5
n
5
DPP
5
A
SER
6
n
6
SER
6
A
GLY
7
n
7
GLY
7
A
LYS
8
n
8
LYS
8
A
LEU
9
n
9
LEU
9
A
ILE
10
n
10
ILE
10
A
ASP
11
n
11
ASP
11
A
THR
12
n
12
THR
12
A
THR
13
n
13
THR
13
A
ALA
14
n
14
ALA
14
A
author_defined_assembly
1
monomeric
380
-1
1540
A
DPP
5
AMINOSERINE
A
DPP
5
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
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
2
A
A
C
OXT
ALA
ALA
14
14
0.142
0.019
1.229
1.371
N
3
A
A
C
OXT
ALA
ALA
14
14
0.138
0.019
1.229
1.367
N
4
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
5
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
6
A
A
C
OXT
ALA
ALA
14
14
0.139
0.019
1.229
1.368
N
7
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
8
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
9
A
A
C
OXT
ALA
ALA
14
14
0.140
0.019
1.229
1.369
N
10
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
11
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
12
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
13
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
14
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
15
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
16
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
17
A
A
C
OXT
ALA
ALA
14
14
0.145
0.019
1.229
1.374
N
18
A
A
C
OXT
ALA
ALA
14
14
0.141
0.019
1.229
1.370
N
19
A
A
C
OXT
ALA
ALA
14
14
0.140
0.019
1.229
1.369
N
20
A
A
C
OXT
ALA
ALA
14
14
0.143
0.019
1.229
1.372
N
1
A
SER
6
-163.20
115.19
1
A
LYS
8
-158.03
-84.61
1
A
THR
13
-100.20
79.82
2
A
SER
6
-162.16
119.04
2
A
LYS
8
-152.98
-85.88
3
A
SER
6
-162.34
113.30
3
A
LYS
8
-160.73
-82.29
3
A
THR
12
-56.00
108.48
4
A
LYS
8
-153.47
-94.93
4
A
THR
12
-57.84
102.93
5
A
SER
6
-162.14
108.37
5
A
LYS
8
-154.53
-92.03
5
A
THR
12
-69.39
99.48
6
A
SER
6
-166.22
113.93
6
A
LYS
8
-158.46
-85.48
6
A
THR
12
-56.88
108.04
7
A
LYS
8
-159.91
-90.32
8
A
LYS
8
-159.90
-95.03
9
A
LYS
8
-155.06
-90.62
10
A
SER
6
-162.62
111.99
10
A
LYS
8
-150.87
-92.36
10
A
THR
12
-59.46
105.72
11
A
DPP
5
-151.48
82.64
11
A
SER
6
-167.61
113.24
11
A
LYS
8
-148.06
-90.85
12
A
LYS
8
-157.75
-85.81
12
A
THR
13
-93.43
-65.04
13
A
LYS
8
-155.57
-89.19
13
A
THR
13
-97.53
-69.42
14
A
LYS
8
-156.20
-89.53
14
A
THR
13
-130.65
-73.36
15
A
LYS
8
-156.30
-99.34
16
A
LYS
8
-152.49
-93.57
16
A
THR
12
-58.51
104.37
16
A
THR
13
-140.87
-72.72
17
A
LYS
8
-159.50
-91.36
18
A
LYS
8
-161.90
-91.65
19
A
LYS
8
-158.81
-94.38
19
A
THR
13
-142.33
-73.09
20
A
SER
6
-161.00
105.33
20
A
LYS
8
-154.29
-92.43
20
A
THR
13
-132.04
-77.08
Transmembrane protein gp41
Solution structure of lactam analogue DapD of HIV gp41 600-612 loop
1
N
N
covale
1.341
A
ACE
1
A
C
ACE
1
1_555
A
ILE
2
A
N
ILE
2
1_555
covale
1.347
A
GLY
4
A
C
GLY
4
1_555
A
DPP
5
A
N
DPP
5
1_555
covale
1.349
A
DPP
5
A
C
DPP
5
1_555
A
SER
6
A
N
SER
6
1_555
covale
1.343
sing
A
DPP
5
A
NG
DPP
5
1_555
A
ASP
11
A
CG
ASP
11
1_555
VIRAL PROTEIN
cyclic peptide, gp41, HIV, lactam bond, pseudopeptide, Viral protein
ENV_HV1BR
UNP
1
600
P03377
IWGCSGKLICTTA
600
612
1JD8
2
14
P03377
A
1
2
14
1
acetylation
ACE
1
1JD8
A
P03377
UNP
1
1
CYS
engineered mutation
DPP
5
1JD8
A
P03377
UNP
603
5
1
CYS
engineered mutation
ASP
11
1JD8
A
P03377
UNP
609
11