0.017564
0.000000
0.000000
0.000000
0.010757
0.000000
0.000000
0.000000
0.019794
0.000000
0.000000
0.000000
Su, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
90.000
90.000
56.934
92.964
50.521
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 H12 O6
180.156
beta-D-glucopyranose
D-saccharide, beta linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C6 H12 O6
180.156
beta-D-galactopyranose
D-saccharide, beta 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
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
US
Biosci. Rep.
1573-4935
38
10.1042/BSR20181787
30413611
Resetting the ligand binding site of placental protein 13/galectin-13 recovers its ability to bind lactose
2018
0000-0001-8406-1676
100
1
PIXEL
2017-12-23
DECTRIS PILATUS 6M
SINGLE WAVELENGTH
M
x-ray
1
0.977
1.0
BL18U1
SSRF
0.977
SYNCHROTRON
SSRF BEAMLINE BL18U1
16004.324
Galactoside-binding soluble lectin 13
UNP residues 2-139
R53H, H57R
1
man
polymer
342.297
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
1
man
branched
18.015
water
98
nat
water
Galectin-13,Gal-13,Placental tissue protein 13,Placental protein 13
beta-lactose
no
no
SSLPVPYKLPVSLSVGSCVIIKGTPIHSFINDPQLQVDFYTDMDEDSDIAFHFRVRFGNHVVMNRREFGIWMLEETTDYV
PFEDGKQFELCIYVHYNEYEIKVNGIRIYGFVHRIPPSFVKMVQVSRDISLTSVCVCN
SSLPVPYKLPVSLSVGSCVIIKGTPIHSFINDPQLQVDFYTDMDEDSDIAFHFRVRFGNHVVMNRREFGIWMLEETTDYV
PFEDGKQFELCIYVHYNEYEIKVNGIRIYGFVHRIPPSFVKMVQVSRDISLTSVCVCN
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
n
n
n
n
n
n
n
n
n
n
n
n
n
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
sample
1
138
LGALS13, PLAC8
9606
Homo sapiens
562
Escherichia coli
Biological sequence
1
2.09
41.11
VAPOR DIFFUSION, HANGING DROP
PEG
298
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
struct_conn
struct_conn_type
struct_site
struct_site_gen
repository
Initial release
Carbohydrate remediation
repository
Remediation
Atomic model
Data collection
Derived calculations
Non-polymer description
Structure summary
1
0
2018-12-26
2
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_asym_id
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_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.type
China
National Natural Science Foundation of China
31500637
A
B4H
201
n
B
BGC
1
A
B4H
201
n
B
GAL
2
DGlcpb
b-D-glucopyranose
b-D-Glcp
Glc
DGalpb
b-D-galactopyranose
b-D-Galp
Gal
N
PDBJ
Y
PDBJ
2018-06-26
REL
REL
oligosaccharide
DGalpb1-4DGlcpb1-ROH
2
GMML
1.0
Glycam Condensed Sequence
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1
2
PDB2Glycan
1.1.0
WURCS
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}
2
PDB-CARE
LINUCS
C1
O4
GAL
BGC
2
1
2
O1
HO4
sing
n
n
HOH
water
Nutrient
oligosaccharide
beta-lactose
Oligosaccharide
HOH
48
3
HOH
HOH
301
A
HOH
61
3
HOH
HOH
302
A
HOH
86
3
HOH
HOH
303
A
HOH
62
3
HOH
HOH
304
A
HOH
87
3
HOH
HOH
305
A
HOH
64
3
HOH
HOH
306
A
HOH
33
3
HOH
HOH
307
A
HOH
79
3
HOH
HOH
308
A
HOH
72
3
HOH
HOH
309
A
HOH
22
3
HOH
HOH
310
A
HOH
19
3
HOH
HOH
311
A
HOH
89
3
HOH
HOH
312
A
HOH
31
3
HOH
HOH
313
A
HOH
24
3
HOH
HOH
314
A
HOH
96
3
HOH
HOH
315
A
HOH
63
3
HOH
HOH
316
A
HOH
3
3
HOH
HOH
317
A
HOH
84
3
HOH
HOH
318
A
HOH
75
3
HOH
HOH
319
A
HOH
2
3
HOH
HOH
320
A
HOH
8
3
HOH
HOH
321
A
HOH
38
3
HOH
HOH
322
A
HOH
83
3
HOH
HOH
323
A
HOH
35
3
HOH
HOH
324
A
HOH
44
3
HOH
HOH
325
A
HOH
41
3
HOH
HOH
326
A
HOH
73
3
HOH
HOH
327
A
HOH
13
3
HOH
HOH
328
A
HOH
54
3
HOH
HOH
329
A
HOH
7
3
HOH
HOH
330
A
HOH
15
3
HOH
HOH
331
A
HOH
58
3
HOH
HOH
332
A
HOH
60
3
HOH
HOH
333
A
HOH
1
3
HOH
HOH
334
A
HOH
34
3
HOH
HOH
335
A
HOH
21
3
HOH
HOH
336
A
HOH
91
3
HOH
HOH
337
A
HOH
46
3
HOH
HOH
338
A
HOH
23
3
HOH
HOH
339
A
HOH
68
3
HOH
HOH
340
A
HOH
45
3
HOH
HOH
341
A
HOH
11
3
HOH
HOH
342
A
HOH
80
3
HOH
HOH
343
A
HOH
4
3
HOH
HOH
344
A
HOH
53
3
HOH
HOH
345
A
HOH
90
3
HOH
HOH
346
A
HOH
28
3
HOH
HOH
347
A
HOH
20
3
HOH
HOH
348
A
HOH
78
3
HOH
HOH
349
A
HOH
65
3
HOH
HOH
350
A
HOH
50
3
HOH
HOH
351
A
HOH
36
3
HOH
HOH
352
A
HOH
5
3
HOH
HOH
353
A
HOH
74
3
HOH
HOH
354
A
HOH
70
3
HOH
HOH
355
A
HOH
40
3
HOH
HOH
356
A
HOH
39
3
HOH
HOH
357
A
HOH
17
3
HOH
HOH
358
A
HOH
32
3
HOH
HOH
359
A
HOH
26
3
HOH
HOH
360
A
HOH
69
3
HOH
HOH
361
A
HOH
42
3
HOH
HOH
362
A
HOH
37
3
HOH
HOH
363
A
HOH
9
3
HOH
HOH
364
A
HOH
43
3
HOH
HOH
365
A
HOH
18
3
HOH
HOH
366
A
HOH
97
3
HOH
HOH
367
A
HOH
57
3
HOH
HOH
368
A
HOH
16
3
HOH
HOH
369
A
HOH
77
3
HOH
HOH
370
A
HOH
51
3
HOH
HOH
371
A
HOH
6
3
HOH
HOH
372
A
HOH
12
3
HOH
HOH
373
A
HOH
55
3
HOH
HOH
374
A
HOH
30
3
HOH
HOH
375
A
HOH
10
3
HOH
HOH
376
A
HOH
93
3
HOH
HOH
377
A
HOH
25
3
HOH
HOH
378
A
HOH
56
3
HOH
HOH
379
A
HOH
29
3
HOH
HOH
380
A
HOH
81
3
HOH
HOH
381
A
HOH
14
3
HOH
HOH
382
A
HOH
82
3
HOH
HOH
383
A
HOH
27
3
HOH
HOH
384
A
HOH
67
3
HOH
HOH
385
A
HOH
94
3
HOH
HOH
386
A
HOH
88
3
HOH
HOH
387
A
HOH
76
3
HOH
HOH
388
A
HOH
49
3
HOH
HOH
389
A
HOH
66
3
HOH
HOH
390
A
HOH
95
3
HOH
HOH
391
A
HOH
47
3
HOH
HOH
392
A
HOH
71
3
HOH
HOH
393
A
HOH
85
3
HOH
HOH
394
A
HOH
59
3
HOH
HOH
395
A
HOH
52
3
HOH
HOH
396
A
HOH
98
3
HOH
HOH
397
A
HOH
92
3
HOH
HOH
398
A
SER
2
n
1
SER
2
A
SER
3
n
2
SER
3
A
LEU
4
n
3
LEU
4
A
PRO
5
n
4
PRO
5
A
VAL
6
n
5
VAL
6
A
PRO
7
n
6
PRO
7
A
TYR
8
n
7
TYR
8
A
LYS
9
n
8
LYS
9
A
LEU
10
n
9
LEU
10
A
PRO
11
n
10
PRO
11
A
VAL
12
n
11
VAL
12
A
SER
13
n
12
SER
13
A
LEU
14
n
13
LEU
14
A
SER
15
n
14
SER
15
A
VAL
16
n
15
VAL
16
A
GLY
17
n
16
GLY
17
A
SER
18
n
17
SER
18
A
CYS
19
n
18
CYS
19
A
VAL
20
n
19
VAL
20
A
ILE
21
n
20
ILE
21
A
ILE
22
n
21
ILE
22
A
LYS
23
n
22
LYS
23
A
GLY
24
n
23
GLY
24
A
THR
25
n
24
THR
25
A
PRO
26
n
25
PRO
26
A
ILE
27
n
26
ILE
27
A
HIS
28
n
27
HIS
28
A
SER
29
n
28
SER
29
A
PHE
30
n
29
PHE
30
A
ILE
31
n
30
ILE
31
A
ASN
32
n
31
ASN
32
A
ASP
33
n
32
ASP
33
A
PRO
34
n
33
PRO
34
A
GLN
35
n
34
GLN
35
A
LEU
36
n
35
LEU
36
A
GLN
37
n
36
GLN
37
A
VAL
38
n
37
VAL
38
A
ASP
39
n
38
ASP
39
A
PHE
40
n
39
PHE
40
A
TYR
41
n
40
TYR
41
A
THR
42
n
41
THR
42
A
ASP
43
n
42
ASP
43
A
MET
44
n
43
MET
44
A
ASP
45
n
44
ASP
45
A
GLU
46
n
45
GLU
46
A
ASP
47
n
46
ASP
47
A
SER
48
n
47
SER
48
A
ASP
49
n
48
ASP
49
A
ILE
50
n
49
ILE
50
A
ALA
51
n
50
ALA
51
A
PHE
52
n
51
PHE
52
A
HIS
53
n
52
HIS
53
A
PHE
54
n
53
PHE
54
A
ARG
55
n
54
ARG
55
A
VAL
56
n
55
VAL
56
A
ARG
57
n
56
ARG
57
A
PHE
58
n
57
PHE
58
A
GLY
59
n
58
GLY
59
A
ASN
60
n
59
ASN
60
A
HIS
61
n
60
HIS
61
A
VAL
62
n
61
VAL
62
A
VAL
63
n
62
VAL
63
A
MET
64
n
63
MET
64
A
ASN
65
n
64
ASN
65
A
ARG
66
n
65
ARG
66
A
ARG
67
n
66
ARG
67
A
GLU
68
n
67
GLU
68
A
PHE
69
n
68
PHE
69
A
GLY
70
n
69
GLY
70
A
ILE
71
n
70
ILE
71
A
TRP
72
n
71
TRP
72
A
MET
73
n
72
MET
73
A
LEU
74
n
73
LEU
74
A
GLU
75
n
74
GLU
75
A
GLU
76
n
75
GLU
76
A
THR
77
n
76
THR
77
A
THR
78
n
77
THR
78
A
ASP
79
n
78
ASP
79
A
TYR
80
n
79
TYR
80
A
VAL
81
n
80
VAL
81
A
PRO
82
n
81
PRO
82
A
PHE
83
n
82
PHE
83
A
GLU
84
n
83
GLU
84
A
ASP
85
n
84
ASP
85
A
GLY
86
n
85
GLY
86
A
LYS
87
n
86
LYS
87
A
GLN
88
n
87
GLN
88
A
PHE
89
n
88
PHE
89
A
GLU
90
n
89
GLU
90
A
LEU
91
n
90
LEU
91
A
CYS
92
n
91
CYS
92
A
ILE
93
n
92
ILE
93
A
TYR
94
n
93
TYR
94
A
VAL
95
n
94
VAL
95
A
HIS
96
n
95
HIS
96
A
TYR
97
n
96
TYR
97
A
ASN
98
n
97
ASN
98
A
GLU
99
n
98
GLU
99
A
TYR
100
n
99
TYR
100
A
GLU
101
n
100
GLU
101
A
ILE
102
n
101
ILE
102
A
LYS
103
n
102
LYS
103
A
VAL
104
n
103
VAL
104
A
ASN
105
n
104
ASN
105
A
GLY
106
n
105
GLY
106
A
ILE
107
n
106
ILE
107
A
ARG
108
n
107
ARG
108
A
ILE
109
n
108
ILE
109
A
TYR
110
n
109
TYR
110
A
GLY
111
n
110
GLY
111
A
PHE
112
n
111
PHE
112
A
VAL
113
n
112
VAL
113
A
HIS
114
n
113
HIS
114
A
ARG
115
n
114
ARG
115
A
ILE
116
n
115
ILE
116
A
PRO
117
n
116
PRO
117
A
PRO
118
n
117
PRO
118
A
SER
119
n
118
SER
119
A
PHE
120
n
119
PHE
120
A
VAL
121
n
120
VAL
121
A
LYS
122
n
121
LYS
122
A
MET
123
n
122
MET
123
A
VAL
124
n
123
VAL
124
A
GLN
125
n
124
GLN
125
A
VAL
126
n
125
VAL
126
A
SER
127
n
126
SER
127
A
ARG
128
n
127
ARG
128
A
ASP
129
n
128
ASP
129
A
ILE
130
n
129
ILE
130
A
SER
131
n
130
SER
131
A
LEU
132
n
131
LEU
132
A
THR
133
n
132
THR
133
A
SER
134
n
133
SER
134
A
VAL
135
n
134
VAL
135
A
CYS
136
n
135
CYS
136
A
VAL
137
n
136
VAL
137
A
CYS
138
n
137
CYS
138
A
ASN
139
n
138
ASN
139
A
author_and_software_defined_assembly
PISA
2
dimeric
gel filtration
1560
-3
12730
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
4_575
x,-y+2,-z
crystal symmetry operation
0.0000000000
185.9280000000
0.0000000000
A
N
LEU
10
A
N
LEU
9
A
O
VAL
124
A
O
VAL
123
A
O
SER
127
A
O
SER
126
A
N
GLN
37
A
N
GLN
36
A
N
LEU
36
A
N
LEU
35
A
O
VAL
56
A
O
VAL
55
A
N
ARG
57
A
N
ARG
56
A
O
HIS
61
A
O
HIS
60
A
N
GLU
68
A
N
GLU
67
A
O
ILE
71
A
O
ILE
70
A
N
LEU
10
A
N
LEU
9
A
O
VAL
124
A
O
VAL
123
A
O
SER
127
A
O
SER
126
A
N
GLN
37
A
N
GLN
36
A
N
LEU
36
A
N
LEU
35
A
O
VAL
56
A
O
VAL
55
A
N
ARG
57
A
N
ARG
56
A
O
HIS
61
A
O
HIS
60
A
N
MET
64
A
N
MET
63
A
O
GLU
76
A
O
GLU
75
A
O
ILE
109
A
O
ILE
108
A
N
ILE
102
A
N
ILE
101
A
O
LYS
103
A
O
LYS
102
A
N
CYS
92
A
N
CYS
91
A
O
PHE
89
A
O
PHE
88
A
N
GLY
24
A
N
GLY
23
A
N
THR
25
A
N
THR
24
A
O
SER
131
A
O
SER
130
1
A
HOH
314
C
HOH
1
A
HOH
374
C
HOH
1
A
CG2
VAL
62
A
CG2
VAL
61
1
Y
1
A
ASN
60
-134.57
-83.43
1
A
MET
73
-93.17
-156.20
1
A
ARG
128
86.93
-139.29
1
A
ASP
129
-96.63
58.00
73.250
26.8939
15.480
0.2089
0.1797
0.1826
1.6300
18.8940
1707
17077
10.0000
99.7600
0.1700
1
THROUGHOUT
1.360
MOLECULAR REPLACEMENT
24.0800
0.9000
1.1100
1.6300
18.8940
98
1245
45.40
34.86
23
0
1124
138
1.63
18.8940
6A63
17086
1
14.2
6.2
99.8
1.63
1.66
1
refinement
PHENIX
(1.10.1_2155: ???)
N
Galactoside-binding soluble lectin 13
Placental protein 13/galectin-13 variant R53HH57R with Lactose
1
N
N
2
N
N
3
N
N
A
SER
29
A
SER
28
HELX_P
A
ASP
33
A
ASP
32
5
AA1
5
A
PRO
117
A
PRO
116
HELX_P
A
VAL
121
A
VAL
120
5
AA2
5
disulf
2.052
A
CYS
136
A
SG
CYS
135
1_555
A
CYS
138
A
SG
CYS
137
4_575
covale
1.370
both
sing
B
BGC
1
B
O4
BGC
1_555
B
GAL
2
B
C1
GAL
1_555
SUGAR BINDING PROTEIN
Sugar binding protein
A
VAL
6
A
VAL
5
1
A
PRO
7
A
PRO
6
3.40
PP13_HUMAN
UNP
1
2
Q9UHV8
SSLPVPYKLPVSLSVGSCVIIKGTPIHSFINDPQLQVDFYTDMDEDSDIAFRFRVHFGNHVVMNRREFGIWMLEETTDYV
PFEDGKQFELCIYVHYNEYEIKVNGIRIYGFVHRIPPSFVKMVQVSRDISLTSVCVCN
2
139
6A63
2
139
Q9UHV8
A
1
1
138
1
ARG
engineered mutation
HIS
53
6A63
A
Q9UHV8
UNP
53
52
1
HIS
engineered mutation
ARG
57
6A63
A
Q9UHV8
UNP
57
56
6
6
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TYR
8
A
TYR
7
A
PRO
11
A
PRO
10
A
MET
123
A
MET
122
A
ARG
128
A
ARG
127
A
GLN
35
A
GLN
34
A
TYR
41
A
TYR
40
A
ILE
50
A
ILE
49
A
ARG
57
A
ARG
56
A
HIS
61
A
HIS
60
A
GLU
68
A
GLU
67
A
ILE
71
A
ILE
70
A
TRP
72
A
TRP
71
A
TYR
8
A
TYR
7
A
PRO
11
A
PRO
10
A
MET
123
A
MET
122
A
ARG
128
A
ARG
127
A
GLN
35
A
GLN
34
A
TYR
41
A
TYR
40
A
ILE
50
A
ILE
49
A
ARG
57
A
ARG
56
A
HIS
61
A
HIS
60
A
GLU
68
A
GLU
67
A
GLU
76
A
GLU
75
A
THR
78
A
THR
77
A
ILE
107
A
ILE
106
A
VAL
113
A
VAL
112
A
GLU
99
A
GLU
98
A
VAL
104
A
VAL
103
A
PHE
89
A
PHE
88
A
VAL
95
A
VAL
94
A
CYS
19
A
CYS
18
A
PRO
26
A
PRO
25
A
ILE
130
A
ILE
129
A
CYS
138
A
CYS
137
21
C 2 2 2