0.018667
0.000000
0.002259
0.000000
0.016359
0.000000
0.000000
0.000000
0.023870
0.00000
0.00000
0.00000
Ramsland, P.A.
Shan, L.
Moomaw, C.R.
Slaughter, C.A.
Guddat, L.W.
Edmundson, A.B.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.00
96.90
90.00
53.570
61.130
42.200
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
H2 O
18.015
WATER
non-polymer
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
C5 H7 N O3
129.114
n
PYROGLUTAMIC ACID
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
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
Mol.Immunol.
MOIMD5
0921
0161-5890
37
295
310
10.1016/S0161-5890(00)00049-3
11000403
An unusual human IgM antibody with a protruding HCDR3 and high avidity for its peptide ligands.
2000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
288
1
AREA DETECTOR
1990-11-19
SIEMENS
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
SIEMENS
11527.743
IGM MEZ IMMUNOGLOBULIN
LIGHT CHAIN VARIABLE DOMAIN FRAGMENT
1
nat
polymer
13214.604
IGM MEZ IMMUNOGLOBULIN
HEAVY CHAIN VARIABLE DOMAIN FRAGMENT
1
nat
polymer
18.015
water
18
nat
water
no
no
DIQMTQSPSSLSASVGDRVTITCRASQDIRNDLGWYQQKPGKAPKKLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQP
EDFATYYCLQQNSNWTFGQGTKVDIK
DIQMTQSPSSLSASVGDRVTITCRASQDIRNDLGWYQQKPGKAPKKLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQP
EDFATYYCLQQNSNWTFGQGTKVDIK
L
polypeptide(L)
no
yes
(PCA)VQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMHWVRQAPGKGLEWVAVISSDGGNKYYTDSVKGRFTISRNDSK
NTLYLQMNSLRTEDTAVFYCARGNPPYSSGWGGGDYWGQGTMVTVSS
QVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMHWVRQAPGKGLEWVAVISSDGGNKYYTDSVKGRFTISRNDSKNTLY
LQMNSLRTEDTAVFYCARGNPPYSSGWGGGDYWGQGTMVTVSS
H
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
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
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
human
Homo
sample
9606
Homo sapiens
human
Homo
sample
9606
Homo sapiens
1
2.72
55.20
MICROSEEDING, SITTING DROP
7.0
6-8% (W/V) PEG 8000, 0.05% (W/V) SODIUM AZIDE, pH 7.0, MICROSEEDING, SITTING DROP, temperature 295K
295
software
entity_poly
pdbx_struct_mod_residue
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Derived calculations
Polymer sequence
1
0
2000-10-04
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-10-04
2
0
2019-12-25
_entity_poly.pdbx_seq_one_letter_code_can
_pdbx_struct_mod_residue.parent_comp_id
_struct_conn.pdbx_leaving_atom_flag
RCSB
Y
RCSB
2000-01-04
REL
REL
HOH
water
HOH
3
3
HOH
HOH
107
L
HOH
4
3
HOH
HOH
108
L
HOH
5
3
HOH
HOH
109
L
HOH
6
3
HOH
HOH
110
L
HOH
10
3
HOH
HOH
111
L
HOH
11
3
HOH
HOH
112
L
HOH
12
3
HOH
HOH
113
L
HOH
13
3
HOH
HOH
114
L
HOH
14
3
HOH
HOH
115
L
HOH
15
3
HOH
HOH
116
L
HOH
1
3
HOH
HOH
124
H
HOH
2
3
HOH
HOH
125
H
HOH
7
3
HOH
HOH
126
H
HOH
8
3
HOH
HOH
127
H
HOH
9
3
HOH
HOH
128
H
HOH
16
3
HOH
HOH
129
H
HOH
17
3
HOH
HOH
130
H
HOH
18
3
HOH
HOH
131
H
ASP
1
n
1
ASP
1
L
ILE
2
n
2
ILE
2
L
GLN
3
n
3
GLN
3
L
MET
4
n
4
MET
4
L
THR
5
n
5
THR
5
L
GLN
6
n
6
GLN
6
L
SER
7
n
7
SER
7
L
PRO
8
n
8
PRO
8
L
SER
9
n
9
SER
9
L
SER
10
n
10
SER
10
L
LEU
11
n
11
LEU
11
L
SER
12
n
12
SER
12
L
ALA
13
n
13
ALA
13
L
SER
14
n
14
SER
14
L
VAL
15
n
15
VAL
15
L
GLY
16
n
16
GLY
16
L
ASP
17
n
17
ASP
17
L
ARG
18
n
18
ARG
18
L
VAL
19
n
19
VAL
19
L
THR
20
n
20
THR
20
L
ILE
21
n
21
ILE
21
L
THR
22
n
22
THR
22
L
CYS
23
n
23
CYS
23
L
ARG
24
n
24
ARG
24
L
ALA
25
n
25
ALA
25
L
SER
26
n
26
SER
26
L
GLN
27
n
27
GLN
27
L
ASP
28
n
28
ASP
28
L
ILE
29
n
29
ILE
29
L
ARG
30
n
30
ARG
30
L
ASN
31
n
31
ASN
31
L
ASP
32
n
32
ASP
32
L
LEU
33
n
33
LEU
33
L
GLY
34
n
34
GLY
34
L
TRP
35
n
35
TRP
35
L
TYR
36
n
36
TYR
36
L
GLN
37
n
37
GLN
37
L
GLN
38
n
38
GLN
38
L
LYS
39
n
39
LYS
39
L
PRO
40
n
40
PRO
40
L
GLY
41
n
41
GLY
41
L
LYS
42
n
42
LYS
42
L
ALA
43
n
43
ALA
43
L
PRO
44
n
44
PRO
44
L
LYS
45
n
45
LYS
45
L
LYS
46
n
46
LYS
46
L
LEU
47
n
47
LEU
47
L
ILE
48
n
48
ILE
48
L
TYR
49
n
49
TYR
49
L
ALA
50
n
50
ALA
50
L
ALA
51
n
51
ALA
51
L
SER
52
n
52
SER
52
L
SER
53
n
53
SER
53
L
LEU
54
n
54
LEU
54
L
GLN
55
n
55
GLN
55
L
SER
56
n
56
SER
56
L
GLY
57
n
57
GLY
57
L
VAL
58
n
58
VAL
58
L
PRO
59
n
59
PRO
59
L
SER
60
n
60
SER
60
L
ARG
61
n
61
ARG
61
L
PHE
62
n
62
PHE
62
L
SER
63
n
63
SER
63
L
GLY
64
n
64
GLY
64
L
SER
65
n
65
SER
65
L
GLY
66
n
66
GLY
66
L
SER
67
n
67
SER
67
L
GLY
68
n
68
GLY
68
L
THR
69
n
69
THR
69
L
ASP
70
n
70
ASP
70
L
PHE
71
n
71
PHE
71
L
THR
72
n
72
THR
72
L
LEU
73
n
73
LEU
73
L
THR
74
n
74
THR
74
L
ILE
75
n
75
ILE
75
L
SER
76
n
76
SER
76
L
SER
77
n
77
SER
77
L
LEU
78
n
78
LEU
78
L
GLN
79
n
79
GLN
79
L
PRO
80
n
80
PRO
80
L
GLU
81
n
81
GLU
81
L
ASP
82
n
82
ASP
82
L
PHE
83
n
83
PHE
83
L
ALA
84
n
84
ALA
84
L
THR
85
n
85
THR
85
L
TYR
86
n
86
TYR
86
L
TYR
87
n
87
TYR
87
L
CYS
88
n
88
CYS
88
L
LEU
89
n
89
LEU
89
L
GLN
90
n
90
GLN
90
L
GLN
91
n
91
GLN
91
L
ASN
92
n
92
ASN
92
L
SER
93
n
93
SER
93
L
ASN
94
n
94
ASN
94
L
TRP
95
n
95
TRP
95
L
THR
96
n
96
THR
96
L
PHE
97
n
97
PHE
97
L
GLY
98
n
98
GLY
98
L
GLN
99
n
99
GLN
99
L
GLY
100
n
100
GLY
100
L
THR
101
n
101
THR
101
L
LYS
102
n
102
LYS
102
L
VAL
103
n
103
VAL
103
L
ASP
104
n
104
ASP
104
L
ILE
105
n
105
ILE
105
L
LYS
106
n
106
LYS
106
L
PCA
1
n
1
PCA
1
H
VAL
2
n
2
VAL
2
H
GLN
3
n
3
GLN
3
H
LEU
4
n
4
LEU
4
H
VAL
5
n
5
VAL
5
H
GLU
6
n
6
GLU
6
H
SER
7
n
7
SER
7
H
GLY
8
n
8
GLY
8
H
GLY
9
n
9
GLY
9
H
GLY
10
n
10
GLY
10
H
LEU
11
n
11
LEU
11
H
VAL
12
n
12
VAL
12
H
GLN
13
n
13
GLN
13
H
PRO
14
n
14
PRO
14
H
GLY
15
n
15
GLY
15
H
GLY
16
n
16
GLY
16
H
SER
17
n
17
SER
17
H
LEU
18
n
18
LEU
18
H
ARG
19
n
19
ARG
19
H
LEU
20
n
20
LEU
20
H
SER
21
n
21
SER
21
H
CYS
22
n
22
CYS
22
H
ALA
23
n
23
ALA
23
H
ALA
24
n
24
ALA
24
H
SER
25
n
25
SER
25
H
GLY
26
n
26
GLY
26
H
PHE
27
n
27
PHE
27
H
THR
28
n
28
THR
28
H
PHE
29
n
29
PHE
29
H
SER
30
n
30
SER
30
H
SER
31
n
31
SER
31
H
TYR
32
n
32
TYR
32
H
ALA
33
n
33
ALA
33
H
MET
34
n
34
MET
34
H
HIS
35
n
35
HIS
35
H
TRP
36
n
36
TRP
36
H
VAL
37
n
37
VAL
37
H
ARG
38
n
38
ARG
38
H
GLN
39
n
39
GLN
39
H
ALA
40
n
40
ALA
40
H
PRO
41
n
41
PRO
41
H
GLY
42
n
42
GLY
42
H
LYS
43
n
43
LYS
43
H
GLY
44
n
44
GLY
44
H
LEU
45
n
45
LEU
45
H
GLU
46
n
46
GLU
46
H
TRP
47
n
47
TRP
47
H
VAL
48
n
48
VAL
48
H
ALA
49
n
49
ALA
49
H
VAL
50
n
50
VAL
50
H
ILE
51
n
51
ILE
51
H
SER
52
n
52
SER
52
H
SER
53
n
53
SER
53
H
ASP
54
n
54
ASP
54
H
GLY
55
n
55
GLY
55
H
GLY
56
n
56
GLY
56
H
ASN
57
n
57
ASN
57
H
LYS
58
n
58
LYS
58
H
TYR
59
n
59
TYR
59
H
TYR
60
n
60
TYR
60
H
THR
61
n
61
THR
61
H
ASP
62
n
62
ASP
62
H
SER
63
n
63
SER
63
H
VAL
64
n
64
VAL
64
H
LYS
65
n
65
LYS
65
H
GLY
66
n
66
GLY
66
H
ARG
67
n
67
ARG
67
H
PHE
68
n
68
PHE
68
H
THR
69
n
69
THR
69
H
ILE
70
n
70
ILE
70
H
SER
71
n
71
SER
71
H
ARG
72
n
72
ARG
72
H
ASN
73
n
73
ASN
73
H
ASP
74
n
74
ASP
74
H
SER
75
n
75
SER
75
H
LYS
76
n
76
LYS
76
H
ASN
77
n
77
ASN
77
H
THR
78
n
78
THR
78
H
LEU
79
n
79
LEU
79
H
TYR
80
n
80
TYR
80
H
LEU
81
n
81
LEU
81
H
GLN
82
n
82
GLN
82
H
MET
83
n
83
MET
83
H
ASN
84
n
84
ASN
84
H
SER
85
n
85
SER
85
H
LEU
86
n
86
LEU
86
H
ARG
87
n
87
ARG
87
H
THR
88
n
88
THR
88
H
GLU
89
n
89
GLU
89
H
ASP
90
n
90
ASP
90
H
THR
91
n
91
THR
91
H
ALA
92
n
92
ALA
92
H
VAL
93
n
93
VAL
93
H
PHE
94
n
94
PHE
94
H
TYR
95
n
95
TYR
95
H
CYS
96
n
96
CYS
96
H
ALA
97
n
97
ALA
97
H
ARG
98
n
98
ARG
98
H
GLY
99
n
99
GLY
99
H
ASN
100
n
100
ASN
100
H
PRO
101
n
101
PRO
101
H
PRO
102
n
102
PRO
102
H
TYR
103
n
103
TYR
103
H
SER
104
n
104
SER
104
H
SER
105
n
105
SER
105
H
GLY
106
n
106
GLY
106
H
TRP
107
n
107
TRP
107
H
GLY
108
n
108
GLY
108
H
GLY
109
n
109
GLY
109
H
GLY
110
n
110
GLY
110
H
ASP
111
n
111
ASP
111
H
TYR
112
n
112
TYR
112
H
TRP
113
n
113
TRP
113
H
GLY
114
n
114
GLY
114
H
GLN
115
n
115
GLN
115
H
GLY
116
n
116
GLY
116
H
THR
117
n
117
THR
117
H
MET
118
n
118
MET
118
H
VAL
119
n
119
VAL
119
H
THR
120
n
120
THR
120
H
VAL
121
n
121
VAL
121
H
SER
122
n
122
SER
122
H
SER
123
n
123
SER
123
H
author_and_software_defined_assembly
PISA
2
dimeric
1380
-8
10640
H
PCA
1
PYROGLUTAMIC ACID
B
PCA
1
GLN
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
L
N
SER
7
A
N
SER
7
L
O
THR
22
A
O
THR
22
L
O
CYS
23
A
O
CYS
23
L
N
PHE
71
A
N
PHE
71
L
N
THR
74
A
N
THR
74
L
O
SER
63
A
O
SER
63
L
O
SER
53
A
O
SER
53
L
N
TYR
49
A
N
TYR
49
L
N
LEU
47
A
N
LEU
47
L
O
TRP
35
A
O
TRP
35
L
N
GLN
38
A
N
GLN
38
L
O
THR
85
A
O
THR
85
L
N
GLN
90
A
N
GLN
90
L
O
THR
96
A
O
THR
96
L
O
SER
53
A
O
SER
53
L
N
TYR
49
A
N
TYR
49
L
N
LEU
47
A
N
LEU
47
L
O
TRP
35
A
O
TRP
35
L
N
GLN
38
A
N
GLN
38
L
O
THR
85
A
O
THR
85
L
N
TYR
86
A
N
TYR
86
L
O
THR
101
A
O
THR
101
L
N
ASP
104
A
N
ASP
104
L
O
LEU
11
A
O
LEU
11
H
N
SER
7
B
N
SER
7
H
O
SER
21
B
O
SER
21
H
N
CYS
22
B
N
CYS
22
H
O
LEU
79
B
O
LEU
79
H
N
GLN
82
B
N
GLN
82
H
O
THR
69
B
O
THR
69
H
N
VAL
12
B
N
VAL
12
H
O
THR
120
B
O
THR
120
H
N
VAL
119
B
N
VAL
119
H
O
ALA
92
B
O
ALA
92
H
O
ALA
97
B
O
ALA
97
H
N
HIS
35
B
N
HIS
35
H
N
ARG
38
B
N
ARG
38
H
O
GLU
46
B
O
GLU
46
H
O
VAL
50
B
O
VAL
50
H
N
TYR
59
B
N
TYR
59
1
L
ARG
30
55.79
-118.29
1
L
ALA
51
64.30
-43.90
1
L
ALA
84
-179.21
-176.20
1
L
SER
93
-137.25
-149.03
1
H
ASP
74
-68.83
14.35
protein_rep.param
protein.top
pca.par
pca.top
water_rep.param
18.9
0.261
0.009
0.181
0.191
0.191
2.6
20.0
764
6963
6963
11.0
83.4
RANDOM
1
THROUGHOUT
0.0
0.0
ENGH & HUBER
FLAT MODEL
14.31
0.252
0.41
0.28
5.00
0.57
0.38
2.6
20.0
18
1758
0
0
1740
0.007
1.35
27.80
0.78
0.379
0.047
0.286
2.76
65
502
6
11.5
40.6
13.1
2.58
20.0
1DQL
7111
7111
0.0
0.0
0.145
1
12.4
2.25
84.4
0.167
2.58
2.75
1.2
40.0
data scaling
X-GEN
data reduction
X-GEN
phasing
AMoRE
refinement
CNS
IGM MEZ IMMUNOGLOBULIN
CRYSTAL STRUCTURE OF AN UNLIGANDED (NATIVE) FV FROM A HUMAN IGM ANTI-PEPTIDE ANTIBODY
1
N
N
2
N
N
3
N
N
3
N
N
The Mez Fv is a non-covalent heterodimer of VL (chain L) and VH (chain H)
H
THR
28
B
THR
28
HELX_P
H
TYR
32
B
TYR
32
5
1
5
H
ASP
62
B
ASP
62
HELX_P
H
VAL
64
B
VAL
64
5
2
3
H
ARG
87
B
ARG
87
HELX_P
H
THR
91
B
THR
91
5
3
5
disulf
2.030
L
CYS
23
A
SG
CYS
23
1_555
L
CYS
88
A
SG
CYS
88
1_555
disulf
2.032
H
CYS
22
B
SG
CYS
22
1_555
H
CYS
96
B
SG
CYS
96
1_555
covale
1.323
both
H
PCA
1
B
C
PCA
1
1_555
H
VAL
2
B
N
VAL
2
1_555
IMMUNE SYSTEM
IMMUNOGLOBULIN FOLD, ANTIBODY, IgM, Fv, IMMUNE SYSTEM
L
SER
7
A
SER
7
1
L
PRO
8
A
PRO
8
0.88
1DQL
PDB
1
1DQL
1DQL
PDB
2
1DQL
1
106
1DQL
1
106
1DQL
L
1
1
106
1
123
1DQL
1
123
1DQL
H
2
1
123
4
5
6
4
6
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
L
THR
5
A
THR
5
L
SER
7
A
SER
7
L
VAL
19
A
VAL
19
L
ARG
24
A
ARG
24
L
ASP
70
A
ASP
70
L
ILE
75
A
ILE
75
L
PHE
62
A
PHE
62
L
SER
67
A
SER
67
L
SER
53
A
SER
53
L
LEU
54
A
LEU
54
L
LYS
45
A
LYS
45
L
TYR
49
A
TYR
49
L
LEU
33
A
LEU
33
L
GLN
38
A
GLN
38
L
THR
85
A
THR
85
L
GLN
90
A
GLN
90
L
THR
96
A
THR
96
L
PHE
97
A
PHE
97
L
SER
53
A
SER
53
L
LEU
54
A
LEU
54
L
LYS
45
A
LYS
45
L
TYR
49
A
TYR
49
L
LEU
33
A
LEU
33
L
GLN
38
A
GLN
38
L
THR
85
A
THR
85
L
GLN
90
A
GLN
90
L
THR
101
A
THR
101
L
ILE
105
A
ILE
105
L
SER
10
A
SER
10
L
ALA
13
A
ALA
13
H
GLN
3
B
GLN
3
H
SER
7
B
SER
7
H
LEU
18
B
LEU
18
H
SER
25
B
SER
25
H
THR
78
B
THR
78
H
MET
83
B
MET
83
H
PHE
68
B
PHE
68
H
ASN
73
B
ASN
73
H
LEU
11
B
LEU
11
H
VAL
12
B
VAL
12
H
THR
117
B
THR
117
H
VAL
121
B
VAL
121
H
ALA
92
B
ALA
92
H
ARG
98
B
ARG
98
H
MET
34
B
MET
34
H
GLN
39
B
GLN
39
H
LEU
45
B
LEU
45
H
ILE
51
B
ILE
51
H
LYS
58
B
LYS
58
H
TYR
60
B
TYR
60
4
P 1 21 1