1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Bewley, C.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
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
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide 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
C6 H12 O6
180.156
alpha-D-mannopyranose
D-saccharide, alpha linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide 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
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
Structure
STRUE6
2005
0969-2126
9
931
940
10.1016/S0969-2126(01)00653-0
11591348
Solution Structure of a Cyanovirin-N:Man alpha 1-2Man alpha Complex. Structural Basis for High Affinity Carbohydrate-Mediated Binding to gp120
2001
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
11022.090
CYANOVIRIN-N
1
nat
polymer
342.297
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose
2
man
branched
2alpha-alpha-mannobiose
no
no
LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQF
VSTKINLDDHIANIDGTLKYE
LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQF
VSTKINLDDHIANIDGTLKYE
A
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
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Nostoc
sample
45916
Nostoc ellipsosporum
atom_site
chem_comp
entity
entity_name_com
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_molecule_features
pdbx_nonpoly_scheme
pdbx_struct_assembly
pdbx_struct_oper_list
struct_asym
struct_conn
struct_site
struct_site_gen
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Version format compliance
Atomic model
Data collection
Derived calculations
Structure summary
1
0
2001-10-24
1
1
2007-10-21
1
2
2011-07-13
2
0
2020-07-29
_atom_site.auth_asym_id
_atom_site.auth_seq_id
_atom_site.label_asym_id
_chem_comp.name
_chem_comp.type
_entity.formula_weight
_entity.pdbx_description
_entity.pdbx_number_of_molecules
_entity.type
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
MAN
201
n
B
MAN
1
MAN
201
n
B
MAN
2
MAN
202
n
C
MAN
1
MAN
202
n
C
MAN
2
DManpa
a-D-mannopyranose
a-D-Manp
Man
RCSB
Y
RCSB
2001-04-24
REL
oligosaccharide
DManpa1-2DManpa1-ROH
2
GMML
1.0
Glycam Condensed Sequence
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1
2
PDB2Glycan
1.1.0
WURCS
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}
2
PDB-CARE
LINUCS
C1
O2
MAN
MAN
2
1
2
O1
HO2
sing
n
n
RESIDUE NUMBERING:
CVN:1-101
MAN:201/202 (CHAIN B) CORRESPONDS TO
MAN-ALPHA-1,2-MAN-ALPHA BOUND THROUGH THE
HIGH AFFINITY SITE WITH C1-C6 of MAN 201 CORRESPONDING
TO THE REDUCING MANNOPYRANOSE RING AND C1-C6 of MAN 202
CORRESPONDING TO C1-C6 OF THE NONREDUCING PYRANOSE.
MAN:203/204 (CHAIN C) CORRESPONDS TO
MAN-ALPHA-1,2-MAN-ALPHA BOUND THROUGH THE LOW AFFINITY
SITE WITH C1-C6 of MAN 203 CORRESPONDING TO THE REDUCING
MANNOPYRANOSE RING AND C1-C6 of MAN 204 CORRESPONDING
TO C1-C6 OF THE NONREDUCING PYRANOSE.
Metabolism
oligosaccharide
2alpha-alpha-mannobiose
Oligosaccharide
This structure is the restrained regularized mean structure.
IN THIS ENTRY THE ELEVENTH COLUMN OF THE COORDINATES (with "atom" as the first column) REPRESENTS THE AVERAGE RMS
DIFFERENCE BETWEEN THE 50 INDIVIDUAL SIMULATED ANNEALING
STRUCTURES HAVING ZERO DISTANCE VIOLATIONS GREATER THAN
0.2 A AND ZERO DIHEDRAL ANGLE VIOLATIONS GREATER THAN 5 DEG.
THE AVERAGE STRUCTURE WAS GENERATED BY BEST FITTING TO
THE BACKBONE OF RESIDUES 1-101. NOTE THE OCCUPANCY FIELD in the tenth column has no meaning.
AVE.RMS DIFF. TO MEAN FOR INTERFACIAL SIDE CHAINS AND
DISACCHARIDE OF THE HIGH AFFINITY SITE=0.36.
AVE.RMS DIFF. TO MEAN FOR INTERFACIAL SIDE CHAINS AND
DISACCHARIDE OF THE LOW AFFINITY SITE=0.58.
RMS DEVIATIONS FOR BONDS, ANGLES, IMPROPERS, NOE, CDIH
6.389414E-03 0.717363 0.693234 8.897236E-03 9.181435E-02.
50
1
TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN: CBCA(CO)NH
CBCANH
HCCH-COSY
HCCH-TOCSY
15N-SEPARATED HOHAHA
QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS
DIPOLAR COUPLINGS OBTAINED BY TAKING THE DIFFERENCE IN THE J SPLITTINGS IN ISOTROPIC MEDIUM AND IN A LIQUID CRYSTALLINE MEDIUM (5% C12E5, R=0.96) (RUCKERT & OTTING (2000) J.AM.CHEM.SOC. 122, 7793-7797) MEASURED IN 2D IPAP (15N, 1H)-HSQC EXPERIMENTS (OTTIGER ET AL (1998) J.AM.CHEM.SOC. 131, 373-378)
INTERMOLECULAR DISTANCE RESTRAINTS OBTAINED FROM 12C-FILTERED/13C-SEPARATED AND 15N-SEPARATED NOE EXPERIMENTS ON COMPLEXES COMPRISING 1:1 AND 1:2 CVN:MAN-ALPHA-(1,2)-MAN-ALPHA
INTRA-DISACCHARIDE AND INTER-MANNOPYRANOSE DISTANCE RESTRAINTS OBTAINED FROM 12C-FILTERED NOE AND HOHAHA EXPERIMENTS ON COMPLEXES COMPRISING 1:1 AND 1:2 CVN:MAN-ALPHA-(1,2)-MAN-ALPHA.
6.4
300
K
THE STRUCTURE OF THE 1:1 COMPLEX IN WHICH DISACCHARIDE IS BOUND EXCLUSIVELY THROUGH THE HIGH AFFINITY SITE WAS CALCULATED USING CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (BEWLEY AND CLORE (2000) J.AM.CHEM.SOC. 122, 6009-6016; WANG ET AL. (2001) EMBO. J., 19, 5635-5649 & REFS THEREIN) IN WHICH THE PROTEIN BACKBONE AND NON-INTERFACIAL SIDE CHAINS ARE HELD FIXED AND THE DISACCHARIDE AND INTERFACIAL SIDE CHAINS ARE FREE TO TRANSLATE AND ROTATE SUBJECT TO EXPERIMENTAL DISTANCE AND TORSION ANGLE RESTRAINTS. THE STRUCTURE OF THE DISACCHARIDE BOUND THROUGH THE LOW AFFINITY SITE IS A MODEL CALCULATED FROM A COMBINATION OF EXPERIMENTAL DISTANCE AND TORSION ANGLE RESTRAINTS, AND ADDITIONAL RESTRAINTS INTRODUCED ON THE BASIS OF SYMMETRY PRESENT BETWEEN THE TWO DOMAINS (HIGH AND LOW AFFINITY). THE NMR COORDINATES FOR MONOMERIC CVN (PDB ACC. 2EZM) WERE USED FOR THE STARTING COORDINATES WITH 2 EQ. OF MAN-ALPHA-1,2-MAN-ALPHA POSITIONED WITHIN 10 A OF THE PREVIOUSLY MAPPED CARBOHYDRATE BINDING SITES (BEWLEY & OTERO-QUINTERO (2001) J.AM.CHEM.SOC. IN PRESS).
CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS
BRUNGER
refinement
X-PLOR
NIH
500
Bruker
DMX500
600
Bruker
DMX600
LEU
1
n
1
LEU
1
A
GLY
2
n
2
GLY
2
A
LYS
3
n
3
LYS
3
A
PHE
4
n
4
PHE
4
A
SER
5
n
5
SER
5
A
GLN
6
n
6
GLN
6
A
THR
7
n
7
THR
7
A
CYS
8
n
8
CYS
8
A
TYR
9
n
9
TYR
9
A
ASN
10
n
10
ASN
10
A
SER
11
n
11
SER
11
A
ALA
12
n
12
ALA
12
A
ILE
13
n
13
ILE
13
A
GLN
14
n
14
GLN
14
A
GLY
15
n
15
GLY
15
A
SER
16
n
16
SER
16
A
VAL
17
n
17
VAL
17
A
LEU
18
n
18
LEU
18
A
THR
19
n
19
THR
19
A
SER
20
n
20
SER
20
A
THR
21
n
21
THR
21
A
CYS
22
n
22
CYS
22
A
GLU
23
n
23
GLU
23
A
ARG
24
n
24
ARG
24
A
THR
25
n
25
THR
25
A
ASN
26
n
26
ASN
26
A
GLY
27
n
27
GLY
27
A
GLY
28
n
28
GLY
28
A
TYR
29
n
29
TYR
29
A
ASN
30
n
30
ASN
30
A
THR
31
n
31
THR
31
A
SER
32
n
32
SER
32
A
SER
33
n
33
SER
33
A
ILE
34
n
34
ILE
34
A
ASP
35
n
35
ASP
35
A
LEU
36
n
36
LEU
36
A
ASN
37
n
37
ASN
37
A
SER
38
n
38
SER
38
A
VAL
39
n
39
VAL
39
A
ILE
40
n
40
ILE
40
A
GLU
41
n
41
GLU
41
A
ASN
42
n
42
ASN
42
A
VAL
43
n
43
VAL
43
A
ASP
44
n
44
ASP
44
A
GLY
45
n
45
GLY
45
A
SER
46
n
46
SER
46
A
LEU
47
n
47
LEU
47
A
LYS
48
n
48
LYS
48
A
TRP
49
n
49
TRP
49
A
GLN
50
n
50
GLN
50
A
PRO
51
n
51
PRO
51
A
SER
52
n
52
SER
52
A
ASN
53
n
53
ASN
53
A
PHE
54
n
54
PHE
54
A
ILE
55
n
55
ILE
55
A
GLU
56
n
56
GLU
56
A
THR
57
n
57
THR
57
A
CYS
58
n
58
CYS
58
A
ARG
59
n
59
ARG
59
A
ASN
60
n
60
ASN
60
A
THR
61
n
61
THR
61
A
GLN
62
n
62
GLN
62
A
LEU
63
n
63
LEU
63
A
ALA
64
n
64
ALA
64
A
GLY
65
n
65
GLY
65
A
SER
66
n
66
SER
66
A
SER
67
n
67
SER
67
A
GLU
68
n
68
GLU
68
A
LEU
69
n
69
LEU
69
A
ALA
70
n
70
ALA
70
A
ALA
71
n
71
ALA
71
A
GLU
72
n
72
GLU
72
A
CYS
73
n
73
CYS
73
A
LYS
74
n
74
LYS
74
A
THR
75
n
75
THR
75
A
ARG
76
n
76
ARG
76
A
ALA
77
n
77
ALA
77
A
GLN
78
n
78
GLN
78
A
GLN
79
n
79
GLN
79
A
PHE
80
n
80
PHE
80
A
VAL
81
n
81
VAL
81
A
SER
82
n
82
SER
82
A
THR
83
n
83
THR
83
A
LYS
84
n
84
LYS
84
A
ILE
85
n
85
ILE
85
A
ASN
86
n
86
ASN
86
A
LEU
87
n
87
LEU
87
A
ASP
88
n
88
ASP
88
A
ASP
89
n
89
ASP
89
A
HIS
90
n
90
HIS
90
A
ILE
91
n
91
ILE
91
A
ALA
92
n
92
ALA
92
A
ASN
93
n
93
ASN
93
A
ILE
94
n
94
ILE
94
A
ASP
95
n
95
ASP
95
A
GLY
96
n
96
GLY
96
A
THR
97
n
97
THR
97
A
LEU
98
n
98
LEU
98
A
LYS
99
n
99
LYS
99
A
TYR
100
n
100
TYR
100
A
GLU
101
n
101
GLU
101
A
author_defined_assembly
1
monomeric
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
A
O
GLN
14
A
O
GLN
14
A
N
VAL
17
A
N
VAL
17
A
O
CYS
22
A
O
CYS
22
A
N
ASN
30
A
N
ASN
30
A
N
VAL
43
A
N
VAL
43
A
O
SER
46
A
O
SER
46
A
N
ALA
64
A
N
ALA
64
A
O
GLU
68
A
O
GLU
68
A
O
CYS
73
A
O
CYS
73
A
N
VAL
81
A
N
VAL
81
A
N
ILE
94
A
N
ILE
94
A
O
THR
97
A
O
THR
97
1
A
SER
52
174.41
12.36
CYANOVIRIN-N
Solution NMR Structure of Complex of 1:2 Cyanovirin-N:Man-Alpha1,2-Man-Alpha Restrained Regularized Mean Coordinates
1
N
N
2
N
N
2
N
N
A
LYS
3
A
LYS
3
HELX_P
A
GLN
6
A
GLN
6
5
1
4
A
ASN
53
A
ASN
53
HELX_P
A
GLU
56
A
GLU
56
5
2
4
disulf
2.023
A
CYS
8
A
SG
CYS
8
1_555
A
CYS
22
A
SG
CYS
22
1_555
disulf
2.019
A
CYS
58
A
SG
CYS
58
1_555
A
CYS
73
A
SG
CYS
73
1_555
covale
1.443
both
B
MAN
1
B
O2
MAN
1_555
B
MAN
2
B
C1
MAN
1_555
covale
1.442
both
C
MAN
1
C
O2
MAN
1_555
C
MAN
2
C
C1
MAN
1_555
ANTIVIRAL PROTEIN
HIV-INACTIVATING PROTEIN, MAN-ALPHA1, 2-MAN-ALPHA, ANTIVIRAL PROTEIN
CVN_NOSEL
UNP
1
1
P81180
LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQF
VSTKINLDDHIANIDGTLKYE
1
101
1IIY
1
101
P81180
A
1
1
101
3
2
3
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
CYS
8
A
CYS
8
A
GLN
14
A
GLN
14
A
VAL
17
A
VAL
17
A
GLU
23
A
GLU
23
A
TYR
29
A
TYR
29
A
ASP
35
A
ASP
35
A
ILE
40
A
ILE
40
A
VAL
43
A
VAL
43
A
SER
46
A
SER
46
A
TRP
49
A
TRP
49
A
CYS
58
A
CYS
58
A
ALA
64
A
ALA
64
A
GLU
68
A
GLU
68
A
LYS
74
A
LYS
74
A
PHE
80
A
PHE
80
A
ASN
86
A
ASN
86
A
ILE
91
A
ILE
91
A
ILE
94
A
ILE
94
A
THR
97
A
THR
97
A
TYR
100
A
TYR
100