0.022777
0.000000
0.000000
0.000000
0.016822
0.000000
0.000000
0.000000
0.010140
0.00000
0.00000
0.00000
Lee, S.-C.
Guan, H.-H.
Wang, C.-H.
Huang, W.-N.
Chen, C.-J.
Wu, W.-G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
43.903
59.447
98.620
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
C6 H8 O7
192.124
CITRIC ACID
non-polymer
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
H2 O
18.015
WATER
non-polymer
C6 H10 O10 S
274.203
n
2-O-sulfo-alpha-L-idopyranuronic acid
O2-SULFO-GLUCURONIC ACID
L-saccharide, alpha 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
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
C6 H13 N O11 S2
339.298
n
2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose
D-saccharide, alpha linking
C4 H9 N O3
119.119
y
THREONINE
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
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
280
9567
9577
10.1074/jbc.M412398200
15590643
Structural basis of citrate-dependent and heparan sulfate-mediated cell surface retention of cobra cardiotoxin A3
2005
IDS C 6 HAS WRONG CHIRALITY AT ATOM C5
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
110
1
IMAGE PLATE
2004-07-15
MARRESEARCH
Si 111 CHANNEL
SINGLE WAVELENGTH
M
x-ray
1
1.1274
1.0
BL17B2
NSRRC
1.1274
SYNCHROTRON
NSRRC BEAMLINE BL17B2
6758.330
Cytotoxin 3
2
nat
polymer
1750.427
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose
1
man
branched
192.124
CITRIC ACID
1
syn
non-polymer
18.015
water
10
nat
water
Cardiotoxin 3, CTX-3, Cardiotoxin analog III, CTX III
no
no
LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
A,B
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
Chinese cobra
Naja
sample
8656
Naja atra
1
1.893
35.07
VAPOR DIFFUSION, HANGING DROP
5.6
PEG4000, isopropanol, trisodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
software
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
struct_asym
struct_conn
struct_site
struct_site_gen
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Non-polymer description
Version format compliance
Refinement description
Advisory
Atomic model
Data collection
Derived calculations
Structure summary
1
0
2004-12-14
1
1
2008-04-30
1
2
2011-07-13
1
3
2017-10-11
2
0
2020-07-29
_software.classification
_software.name
_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.mon_nstd_flag
_chem_comp.name
_chem_comp.type
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_unobs_or_zero_occ_atoms.auth_asym_id
_pdbx_unobs_or_zero_occ_atoms.auth_seq_id
_pdbx_unobs_or_zero_occ_atoms.label_seq_id
_pdbx_validate_chiral.auth_asym_id
_pdbx_validate_chiral.auth_seq_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.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
SGN
66
n
C
SGN
1
A
IDS
65
n
C
IDS
2
A
SGN
64
n
C
SGN
3
A
IDS
63
n
C
IDS
4
A
SGN
62
n
C
SGN
5
A
IDS
61
n
C
IDS
6
a-L-IdopA2SO3
DGlcpNS[6S]a
N-sulfo-6-sulfo-a-D-glucopyranose
a-D-GlcpNSO36SO3
RCSB
Y
PDBJ
2004-10-21
REL
oligosaccharide
WURCS=2.0/2,6,5/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-1-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1
2
PDB2Glycan
1.1.0
WURCS
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}}}}}
2
PDB-CARE
LINUCS
C1
O4
IDS
SGN
2
1
2
O1
HO4
sing
C1
O4
SGN
IDS
3
2
2
O1
HO4
sing
C1
O4
IDS
SGN
4
3
2
O1
HO4
sing
C1
O4
SGN
IDS
5
4
2
O1
HO4
sing
C1
O4
IDS
SGN
6
5
2
O1
HO4
sing
n
n
n
n
n
n
CIT
CITRIC ACID
HOH
water
CIT
101
3
CIT
CIT
101
A
HOH
102
4
HOH
HOH
102
A
HOH
103
4
HOH
HOH
103
A
HOH
104
4
HOH
HOH
104
A
HOH
105
4
HOH
HOH
105
A
HOH
106
4
HOH
HOH
106
A
HOH
107
4
HOH
HOH
107
A
HOH
108
4
HOH
HOH
108
A
HOH
109
4
HOH
HOH
109
A
HOH
110
4
HOH
HOH
110
A
HOH
61
4
HOH
HOH
61
B
LEU
1
n
1
LEU
1
A
LYS
2
n
2
LYS
2
A
CYS
3
n
3
CYS
3
A
ASN
4
n
4
ASN
4
A
LYS
5
n
5
LYS
5
A
LEU
6
n
6
LEU
6
A
VAL
7
n
7
VAL
7
A
PRO
8
n
8
PRO
8
A
LEU
9
n
9
LEU
9
A
PHE
10
n
10
PHE
10
A
TYR
11
n
11
TYR
11
A
LYS
12
n
12
LYS
12
A
THR
13
n
13
THR
13
A
CYS
14
n
14
CYS
14
A
PRO
15
n
15
PRO
15
A
ALA
16
n
16
ALA
16
A
GLY
17
n
17
GLY
17
A
LYS
18
n
18
LYS
18
A
ASN
19
n
19
ASN
19
A
LEU
20
n
20
LEU
20
A
CYS
21
n
21
CYS
21
A
TYR
22
n
22
TYR
22
A
LYS
23
n
23
LYS
23
A
MET
24
n
24
MET
24
A
PHE
25
n
25
PHE
25
A
MET
26
n
26
MET
26
A
VAL
27
n
27
VAL
27
A
ALA
28
n
28
ALA
28
A
THR
29
n
29
THR
29
A
PRO
30
n
30
PRO
30
A
LYS
31
n
31
LYS
31
A
VAL
32
n
32
VAL
32
A
PRO
33
n
33
PRO
33
A
VAL
34
n
34
VAL
34
A
LYS
35
n
35
LYS
35
A
ARG
36
n
36
ARG
36
A
GLY
37
n
37
GLY
37
A
CYS
38
n
38
CYS
38
A
ILE
39
n
39
ILE
39
A
ASP
40
n
40
ASP
40
A
VAL
41
n
41
VAL
41
A
CYS
42
n
42
CYS
42
A
PRO
43
n
43
PRO
43
A
LYS
44
n
44
LYS
44
A
SER
45
n
45
SER
45
A
SER
46
n
46
SER
46
A
LEU
47
n
47
LEU
47
A
LEU
48
n
48
LEU
48
A
VAL
49
n
49
VAL
49
A
LYS
50
n
50
LYS
50
A
TYR
51
n
51
TYR
51
A
VAL
52
n
52
VAL
52
A
CYS
53
n
53
CYS
53
A
CYS
54
n
54
CYS
54
A
ASN
55
n
55
ASN
55
A
THR
56
n
56
THR
56
A
ASP
57
n
57
ASP
57
A
ARG
58
n
58
ARG
58
A
CYS
59
n
59
CYS
59
A
ASN
60
n
60
ASN
60
A
LEU
1
n
1
LEU
1
B
LYS
2
n
2
LYS
2
B
CYS
3
n
3
CYS
3
B
ASN
4
n
4
ASN
4
B
LYS
5
n
5
LYS
5
B
LEU
6
n
6
LEU
6
B
VAL
7
n
7
VAL
7
B
PRO
8
n
8
PRO
8
B
LEU
9
n
9
LEU
9
B
PHE
10
n
10
PHE
10
B
TYR
11
n
11
TYR
11
B
LYS
12
n
12
LYS
12
B
THR
13
n
13
THR
13
B
CYS
14
n
14
CYS
14
B
PRO
15
n
15
PRO
15
B
ALA
16
n
16
ALA
16
B
GLY
17
n
17
GLY
17
B
LYS
18
n
18
LYS
18
B
ASN
19
n
19
ASN
19
B
LEU
20
n
20
LEU
20
B
CYS
21
n
21
CYS
21
B
TYR
22
n
22
TYR
22
B
LYS
23
n
23
LYS
23
B
MET
24
n
24
MET
24
B
PHE
25
n
25
PHE
25
B
MET
26
n
26
MET
26
B
VAL
27
n
27
VAL
27
B
ALA
28
n
28
ALA
28
B
THR
29
n
29
THR
29
B
PRO
30
n
30
PRO
30
B
LYS
31
n
31
LYS
31
B
VAL
32
n
32
VAL
32
B
PRO
33
n
33
PRO
33
B
VAL
34
n
34
VAL
34
B
LYS
35
n
35
LYS
35
B
ARG
36
n
36
ARG
36
B
GLY
37
n
37
GLY
37
B
CYS
38
n
38
CYS
38
B
ILE
39
n
39
ILE
39
B
ASP
40
n
40
ASP
40
B
VAL
41
n
41
VAL
41
B
CYS
42
n
42
CYS
42
B
PRO
43
n
43
PRO
43
B
LYS
44
n
44
LYS
44
B
SER
45
n
45
SER
45
B
SER
46
n
46
SER
46
B
LEU
47
n
47
LEU
47
B
LEU
48
n
48
LEU
48
B
VAL
49
n
49
VAL
49
B
LYS
50
n
50
LYS
50
B
TYR
51
n
51
TYR
51
B
VAL
52
n
52
VAL
52
B
CYS
53
n
53
CYS
53
B
CYS
54
n
54
CYS
54
B
ASN
55
n
55
ASN
55
B
THR
56
n
56
THR
56
B
ASP
57
n
57
ASP
57
B
ARG
58
n
58
ARG
58
B
CYS
59
n
59
CYS
59
B
ASN
60
n
60
ASN
60
B
author_and_software_defined_assembly
PISA
2
dimeric
2780
-1
8100
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
7_555
-x+1/2,y+1/2,-z+1/2
crystal symmetry operation
21.9515000000
29.7235000000
49.3100000000
A
N
CYS
3
A
N
CYS
3
A
O
LYS
12
A
O
LYS
12
A
O
GLY
37
A
O
GLY
37
A
N
TYR
22
A
N
TYR
22
A
N
LYS
23
A
N
LYS
23
A
O
VAL
52
A
O
VAL
52
B
O
LYS
35
B
O
LYS
35
B
N
MET
24
B
N
MET
24
B
N
CYS
21
B
N
CYS
21
B
O
CYS
54
B
O
CYS
54
1
C
O4
IDS
6
C
O4
IDS
6
1
N
1
C
C5
IDS
6
PLANAR
1
A
A
O2
O2
CIT
CIT
101
101
2.19
1_555
3_555
1
A
LEU
9
-60.89
2.30
1
A
ALA
16
-31.28
135.49
1
A
LYS
18
-52.28
92.70
1
A
ASN
19
-105.25
49.61
1
A
SER
46
-93.65
-134.16
1
A
LEU
47
-98.26
-62.58
1
B
THR
13
-50.01
103.49
1
B
PRO
15
-59.33
-179.01
1
B
VAL
27
-20.26
-43.15
1
B
THR
29
-150.31
73.82
1
B
VAL
32
-102.68
64.26
1
B
ASP
40
-61.42
-90.97
1
B
SER
45
-80.87
-159.55
1
B
SER
46
-148.17
-157.71
0.25
0.227
0.242
0.231
2.4
25
245
5051
4889
RANDOM
1
0
MOLECULAR REPLACEMENT
Engh & Huber
2.4
25
10
1058
118
0
930
0.005
1.170
2.4
25
1XT3
5051
4889
0
0
0.038
1
4.1
96.8
2.4
2.48
1
83.6
data scaling
XDS
data scaling
SCALEPACK
refinement
CNS
data reduction
XDS
phasing
CNS
Cytotoxin 3
Structure Basis of Venom Citrate-Dependent Heparin Sulfate-Mediated Cell Surface Retention of Cobra Cardiotoxin A3
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
disulf
2.027
A
CYS
3
A
SG
CYS
3
1_555
A
CYS
21
A
SG
CYS
21
1_555
disulf
2.029
A
CYS
14
A
SG
CYS
14
1_555
A
CYS
38
A
SG
CYS
38
1_555
disulf
2.029
A
CYS
42
A
SG
CYS
42
1_555
A
CYS
53
A
SG
CYS
53
1_555
disulf
2.023
A
CYS
54
A
SG
CYS
54
1_555
A
CYS
59
A
SG
CYS
59
1_555
disulf
2.030
B
CYS
3
B
SG
CYS
3
1_555
B
CYS
14
B
SG
CYS
14
1_555
disulf
2.027
B
CYS
3
B
SG
CYS
3
1_555
B
CYS
21
B
SG
CYS
21
1_555
disulf
2.026
B
CYS
14
B
SG
CYS
14
1_555
B
CYS
38
B
SG
CYS
38
1_555
disulf
2.031
B
CYS
42
B
SG
CYS
42
1_555
B
CYS
53
B
SG
CYS
53
1_555
disulf
2.029
B
CYS
54
B
SG
CYS
54
1_555
B
CYS
59
B
SG
CYS
59
1_555
covale
1.420
both
C
SGN
1
C
O4
SGN
1_555
C
IDS
2
C
C1
IDS
1_555
covale
1.428
both
C
IDS
2
C
O4
IDS
1_555
C
SGN
3
C
C1
SGN
1_555
covale
1.461
both
C
SGN
3
C
O4
SGN
1_555
C
IDS
4
C
C1
IDS
1_555
covale
1.433
both
C
IDS
4
C
O4
IDS
1_555
C
SGN
5
C
C1
SGN
1_555
covale
1.442
both
C
SGN
5
C
O4
SGN
1_555
C
IDS
6
C
C1
IDS
1_555
TOXIN
CTX-3, heparin, citrate, Toxin
CTX3_NAJAT
UNP
1
22
P60301
LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
22
81
1XT3
1
60
P60301
A
1
1
60
22
81
1XT3
1
60
P60301
B
1
1
60
2
3
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LYS
2
A
LYS
2
A
ASN
4
A
ASN
4
A
TYR
11
A
TYR
11
A
THR
13
A
THR
13
A
LYS
35
A
LYS
35
A
CYS
38
A
CYS
38
A
CYS
21
A
CYS
21
A
MET
26
A
MET
26
A
VAL
49
A
VAL
49
A
CYS
54
A
CYS
54
B
LYS
35
B
LYS
35
B
CYS
38
B
CYS
38
B
CYS
21
B
CYS
21
B
MET
26
B
MET
26
B
VAL
49
B
VAL
49
B
CYS
54
B
CYS
54
20
C 2 2 21