0.019478
0.000000
0.001570
0.000000
0.016485
0.000000
0.000000
0.000000
0.016512
0.00000
0.00000
0.00000
Hsiao, C.D.
Sun, Y.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.00
94.61
90.00
51.340
60.660
60.760
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
C6 H13 N O5
179.171
2-amino-2-deoxy-beta-D-glucopyranose
2-AMINO-2-DEOXY-D-GLUCOSE
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
J.Biol.Chem.
JBCHA3
0071
0021-9258
276
17507
10.1074/JBC.M010416200
11278670
The Crystal Structure of a Novel Mammalian Lectin, Ym1, Suggests a Saccharide Binding Site
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
290.0
1
MIRRORS
IMAGE PLATE
1997-01-15
RIGAKU IMAGE PLATE
NI FILTER
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU300
42365.516
YM1 SECRETORY PROTEIN
1
nat
polymer
179.171
2-amino-2-deoxy-beta-D-glucopyranose
1
man
non-polymer
18.015
water
214
nat
water
no
no
YQLMCYYTSWAKDRPIEGSFKPGNIDPCLCTHLIYAFAGMQNNEITYTHEQDLRDYEALNGLKDKNTELKTLLAIGGWKF
GPAPFSAMVSTPQNRQIFIQSVIRFLRQYNFDGLNLDWQYPGSRGSPPKDKHLFSVLVKEMRKAFEEESVEKDIPRLLLT
STGAGIIDVIKSGYKIPELSQSLDYIQVMTYDLHDPKDGYTGENSPLYKSPYDIGKSADLNVDSIISYWKDHGAASEKLI
VGFPAYGHTFILSDPSKTGIGAPTISTGPPGKYTDESGLLAYYEVCTFLNEGATEVWDAPQEVPYAYQGNEWVGYDNVRS
FKLKAQWLKDNNLGGAVVWPLDMDDFSGSFCHQRHFPLTSTLKGDLNIHSASCKGPY
YQLMCYYTSWAKDRPIEGSFKPGNIDPCLCTHLIYAFAGMQNNEITYTHEQDLRDYEALNGLKDKNTELKTLLAIGGWKF
GPAPFSAMVSTPQNRQIFIQSVIRFLRQYNFDGLNLDWQYPGSRGSPPKDKHLFSVLVKEMRKAFEEESVEKDIPRLLLT
STGAGIIDVIKSGYKIPELSQSLDYIQVMTYDLHDPKDGYTGENSPLYKSPYDIGKSADLNVDSIISYWKDHGAASEKLI
VGFPAYGHTFILSDPSKTGIGAPTISTGPPGKYTDESGLLAYYEVCTFLNEGATEVWDAPQEVPYAYQGNEWVGYDNVRS
FKLKAQWLKDNNLGGAVVWPLDMDDFSGSFCHQRHFPLTSTLKGDLNIHSASCKGPY
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
HOUSE MOUSE
ORAL INFECTIONS OF MICE WITH TRICHINELLA SPIRALIS INDUCE PERITONEAL EXUDATE CELLS TO SECRETE YM1
sample
PERITONEAL EXUDATE CELLS(MACROPHAGES)
CYTOPLASM
10090
MUS MUSCULUS
ICR
1
2.19
44
6.00
pH 6.00
atom_site
pdbx_database_proc
pdbx_database_status
refine
struct_conn
chem_comp
pdbx_database_status
pdbx_validate_close_contact
struct_conn
struct_conn_type
chem_comp
entity
pdbx_chem_comp_identifier
pdbx_entity_nonpoly
struct_site
struct_site_gen
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Version format compliance
Atomic model
Data collection
Derived calculations
Other
Refinement description
Advisory
Data collection
Derived calculations
Other
Data collection
Derived calculations
Structure summary
1
0
2001-03-01
1
1
2011-05-08
1
2
2011-07-13
2
0
2019-05-22
2
1
2020-07-01
2
2
2020-07-29
_pdbx_database_status.recvd_author_approval
_refine.pdbx_ls_cross_valid_method
_struct_conn.pdbx_leaving_atom_flag
_chem_comp.type
_pdbx_database_status.status_code_sf
_chem_comp.name
_entity.pdbx_description
_pdbx_entity_nonpoly.name
DGlcpNb
b-D-glucopyranosamine
b-D-GlcpN
GlcN
SHEET
DETERMINATION METHOD: DSSP
THE SHEETS PRESENTED AS "A" IN EACH CHAIN ON SHEET RECORDS
BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY
A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS
ARE IDENTICAL.
PDBE
Y
PDBE
2000-10-21
REL
REL
1
A
O
HOH
2006
7.58
1
A
O
HOH
2010
9.13
1
A
O
HOH
2016
7.33
1
A
O
HOH
2019
9.78
1
A
O
HOH
2021
8.62
1
A
O
HOH
2025
6.26
1
A
O
HOH
2030
9.46
1
A
O
HOH
2031
7.61
1
A
O
HOH
2036
6.61
1
A
O
HOH
2037
6.41
1
A
O
HOH
2040
7.37
1
A
O
HOH
2049
8.21
1
A
O
HOH
2055
6.40
1
A
O
HOH
2066
6.22
1
A
O
HOH
2076
6.49
1
A
O
HOH
2081
6.90
1
A
O
HOH
2091
6.26
1
A
O
HOH
2097
6.26
GCS
2-amino-2-deoxy-beta-D-glucopyranose
HOH
water
RESIDUES 394-398 WERE NOT VISIBLE IN THE ELECTRON DENSITY.
HOWEVER, AS THERE IS NO EVIDENCE TO SUGGEST THAT THESE
RESIDUES ARE NOT PRESENT IN THE SAMPLE THEY HAVE BEEN
INCLUDED IN THE SEQRES RECORD.
GCS
800
2
GCS
GCS
800
A
HOH
2001
3
HOH
HOH
2001
A
HOH
2002
3
HOH
HOH
2002
A
HOH
2003
3
HOH
HOH
2003
A
HOH
2004
3
HOH
HOH
2004
A
HOH
2005
3
HOH
HOH
2005
A
HOH
2006
3
HOH
HOH
2006
A
HOH
2007
3
HOH
HOH
2007
A
HOH
2008
3
HOH
HOH
2008
A
HOH
2009
3
HOH
HOH
2009
A
HOH
2010
3
HOH
HOH
2010
A
HOH
2011
3
HOH
HOH
2011
A
HOH
2012
3
HOH
HOH
2012
A
HOH
2013
3
HOH
HOH
2013
A
HOH
2014
3
HOH
HOH
2014
A
HOH
2015
3
HOH
HOH
2015
A
HOH
2016
3
HOH
HOH
2016
A
HOH
2017
3
HOH
HOH
2017
A
HOH
2018
3
HOH
HOH
2018
A
HOH
2019
3
HOH
HOH
2019
A
HOH
2020
3
HOH
HOH
2020
A
HOH
2021
3
HOH
HOH
2021
A
HOH
2022
3
HOH
HOH
2022
A
HOH
2023
3
HOH
HOH
2023
A
HOH
2024
3
HOH
HOH
2024
A
HOH
2025
3
HOH
HOH
2025
A
HOH
2026
3
HOH
HOH
2026
A
HOH
2027
3
HOH
HOH
2027
A
HOH
2028
3
HOH
HOH
2028
A
HOH
2029
3
HOH
HOH
2029
A
HOH
2030
3
HOH
HOH
2030
A
HOH
2031
3
HOH
HOH
2031
A
HOH
2032
3
HOH
HOH
2032
A
HOH
2033
3
HOH
HOH
2033
A
HOH
2034
3
HOH
HOH
2034
A
HOH
2035
3
HOH
HOH
2035
A
HOH
2036
3
HOH
HOH
2036
A
HOH
2037
3
HOH
HOH
2037
A
HOH
2038
3
HOH
HOH
2038
A
HOH
2039
3
HOH
HOH
2039
A
HOH
2040
3
HOH
HOH
2040
A
HOH
2041
3
HOH
HOH
2041
A
HOH
2042
3
HOH
HOH
2042
A
HOH
2043
3
HOH
HOH
2043
A
HOH
2044
3
HOH
HOH
2044
A
HOH
2045
3
HOH
HOH
2045
A
HOH
2046
3
HOH
HOH
2046
A
HOH
2047
3
HOH
HOH
2047
A
HOH
2048
3
HOH
HOH
2048
A
HOH
2049
3
HOH
HOH
2049
A
HOH
2050
3
HOH
HOH
2050
A
HOH
2051
3
HOH
HOH
2051
A
HOH
2052
3
HOH
HOH
2052
A
HOH
2053
3
HOH
HOH
2053
A
HOH
2054
3
HOH
HOH
2054
A
HOH
2055
3
HOH
HOH
2055
A
HOH
2056
3
HOH
HOH
2056
A
HOH
2057
3
HOH
HOH
2057
A
HOH
2058
3
HOH
HOH
2058
A
HOH
2059
3
HOH
HOH
2059
A
HOH
2060
3
HOH
HOH
2060
A
HOH
2061
3
HOH
HOH
2061
A
HOH
2062
3
HOH
HOH
2062
A
HOH
2063
3
HOH
HOH
2063
A
HOH
2064
3
HOH
HOH
2064
A
HOH
2065
3
HOH
HOH
2065
A
HOH
2066
3
HOH
HOH
2066
A
HOH
2067
3
HOH
HOH
2067
A
HOH
2068
3
HOH
HOH
2068
A
HOH
2069
3
HOH
HOH
2069
A
HOH
2070
3
HOH
HOH
2070
A
HOH
2071
3
HOH
HOH
2071
A
HOH
2072
3
HOH
HOH
2072
A
HOH
2073
3
HOH
HOH
2073
A
HOH
2074
3
HOH
HOH
2074
A
HOH
2075
3
HOH
HOH
2075
A
HOH
2076
3
HOH
HOH
2076
A
HOH
2077
3
HOH
HOH
2077
A
HOH
2078
3
HOH
HOH
2078
A
HOH
2079
3
HOH
HOH
2079
A
HOH
2080
3
HOH
HOH
2080
A
HOH
2081
3
HOH
HOH
2081
A
HOH
2082
3
HOH
HOH
2082
A
HOH
2083
3
HOH
HOH
2083
A
HOH
2084
3
HOH
HOH
2084
A
HOH
2085
3
HOH
HOH
2085
A
HOH
2086
3
HOH
HOH
2086
A
HOH
2087
3
HOH
HOH
2087
A
HOH
2088
3
HOH
HOH
2088
A
HOH
2089
3
HOH
HOH
2089
A
HOH
2090
3
HOH
HOH
2090
A
HOH
2091
3
HOH
HOH
2091
A
HOH
2092
3
HOH
HOH
2092
A
HOH
2093
3
HOH
HOH
2093
A
HOH
2094
3
HOH
HOH
2094
A
HOH
2095
3
HOH
HOH
2095
A
HOH
2096
3
HOH
HOH
2096
A
HOH
2097
3
HOH
HOH
2097
A
HOH
2098
3
HOH
HOH
2098
A
HOH
2099
3
HOH
HOH
2099
A
HOH
2100
3
HOH
HOH
2100
A
HOH
2101
3
HOH
HOH
2101
A
HOH
2102
3
HOH
HOH
2102
A
HOH
2103
3
HOH
HOH
2103
A
HOH
2104
3
HOH
HOH
2104
A
HOH
2105
3
HOH
HOH
2105
A
HOH
2106
3
HOH
HOH
2106
A
HOH
2107
3
HOH
HOH
2107
A
HOH
2108
3
HOH
HOH
2108
A
HOH
2109
3
HOH
HOH
2109
A
HOH
2110
3
HOH
HOH
2110
A
HOH
2111
3
HOH
HOH
2111
A
HOH
2112
3
HOH
HOH
2112
A
HOH
2113
3
HOH
HOH
2113
A
HOH
2114
3
HOH
HOH
2114
A
HOH
2115
3
HOH
HOH
2115
A
HOH
2116
3
HOH
HOH
2116
A
HOH
2117
3
HOH
HOH
2117
A
HOH
2118
3
HOH
HOH
2118
A
HOH
2119
3
HOH
HOH
2119
A
HOH
2120
3
HOH
HOH
2120
A
HOH
2121
3
HOH
HOH
2121
A
HOH
2122
3
HOH
HOH
2122
A
HOH
2123
3
HOH
HOH
2123
A
HOH
2124
3
HOH
HOH
2124
A
HOH
2125
3
HOH
HOH
2125
A
HOH
2126
3
HOH
HOH
2126
A
HOH
2127
3
HOH
HOH
2127
A
HOH
2128
3
HOH
HOH
2128
A
HOH
2129
3
HOH
HOH
2129
A
HOH
2130
3
HOH
HOH
2130
A
HOH
2131
3
HOH
HOH
2131
A
HOH
2132
3
HOH
HOH
2132
A
HOH
2133
3
HOH
HOH
2133
A
HOH
2134
3
HOH
HOH
2134
A
HOH
2135
3
HOH
HOH
2135
A
HOH
2136
3
HOH
HOH
2136
A
HOH
2137
3
HOH
HOH
2137
A
HOH
2138
3
HOH
HOH
2138
A
HOH
2139
3
HOH
HOH
2139
A
HOH
2140
3
HOH
HOH
2140
A
HOH
2141
3
HOH
HOH
2141
A
HOH
2142
3
HOH
HOH
2142
A
HOH
2143
3
HOH
HOH
2143
A
HOH
2144
3
HOH
HOH
2144
A
HOH
2145
3
HOH
HOH
2145
A
HOH
2146
3
HOH
HOH
2146
A
HOH
2147
3
HOH
HOH
2147
A
HOH
2148
3
HOH
HOH
2148
A
HOH
2149
3
HOH
HOH
2149
A
HOH
2150
3
HOH
HOH
2150
A
HOH
2151
3
HOH
HOH
2151
A
HOH
2152
3
HOH
HOH
2152
A
HOH
2153
3
HOH
HOH
2153
A
HOH
2154
3
HOH
HOH
2154
A
HOH
2155
3
HOH
HOH
2155
A
HOH
2156
3
HOH
HOH
2156
A
HOH
2157
3
HOH
HOH
2157
A
HOH
2158
3
HOH
HOH
2158
A
HOH
2159
3
HOH
HOH
2159
A
HOH
2160
3
HOH
HOH
2160
A
HOH
2161
3
HOH
HOH
2161
A
HOH
2162
3
HOH
HOH
2162
A
HOH
2163
3
HOH
HOH
2163
A
HOH
2164
3
HOH
HOH
2164
A
HOH
2165
3
HOH
HOH
2165
A
HOH
2166
3
HOH
HOH
2166
A
HOH
2167
3
HOH
HOH
2167
A
HOH
2168
3
HOH
HOH
2168
A
HOH
2169
3
HOH
HOH
2169
A
HOH
2170
3
HOH
HOH
2170
A
HOH
2171
3
HOH
HOH
2171
A
HOH
2172
3
HOH
HOH
2172
A
HOH
2173
3
HOH
HOH
2173
A
HOH
2174
3
HOH
HOH
2174
A
HOH
2175
3
HOH
HOH
2175
A
HOH
2176
3
HOH
HOH
2176
A
HOH
2177
3
HOH
HOH
2177
A
HOH
2178
3
HOH
HOH
2178
A
HOH
2179
3
HOH
HOH
2179
A
HOH
2180
3
HOH
HOH
2180
A
HOH
2181
3
HOH
HOH
2181
A
HOH
2182
3
HOH
HOH
2182
A
HOH
2183
3
HOH
HOH
2183
A
HOH
2184
3
HOH
HOH
2184
A
HOH
2185
3
HOH
HOH
2185
A
HOH
2186
3
HOH
HOH
2186
A
HOH
2187
3
HOH
HOH
2187
A
HOH
2188
3
HOH
HOH
2188
A
HOH
2189
3
HOH
HOH
2189
A
HOH
2190
3
HOH
HOH
2190
A
HOH
2191
3
HOH
HOH
2191
A
HOH
2192
3
HOH
HOH
2192
A
HOH
2193
3
HOH
HOH
2193
A
HOH
2194
3
HOH
HOH
2194
A
HOH
2195
3
HOH
HOH
2195
A
HOH
2196
3
HOH
HOH
2196
A
HOH
2197
3
HOH
HOH
2197
A
HOH
2198
3
HOH
HOH
2198
A
HOH
2199
3
HOH
HOH
2199
A
HOH
2200
3
HOH
HOH
2200
A
HOH
2201
3
HOH
HOH
2201
A
HOH
2202
3
HOH
HOH
2202
A
HOH
2203
3
HOH
HOH
2203
A
HOH
2204
3
HOH
HOH
2204
A
HOH
2205
3
HOH
HOH
2205
A
HOH
2206
3
HOH
HOH
2206
A
HOH
2207
3
HOH
HOH
2207
A
HOH
2208
3
HOH
HOH
2208
A
HOH
2209
3
HOH
HOH
2209
A
HOH
2210
3
HOH
HOH
2210
A
HOH
2211
3
HOH
HOH
2211
A
HOH
2212
3
HOH
HOH
2212
A
HOH
2213
3
HOH
HOH
2213
A
HOH
2214
3
HOH
HOH
2214
A
TYR
22
n
1
TYR
22
A
GLN
23
n
2
GLN
23
A
LEU
24
n
3
LEU
24
A
MET
25
n
4
MET
25
A
CYS
26
n
5
CYS
26
A
TYR
27
n
6
TYR
27
A
TYR
28
n
7
TYR
28
A
THR
29
n
8
THR
29
A
SER
30
n
9
SER
30
A
TRP
31
n
10
TRP
31
A
ALA
32
n
11
ALA
32
A
LYS
33
n
12
LYS
33
A
ASP
34
n
13
ASP
34
A
ARG
35
n
14
ARG
35
A
PRO
36
n
15
PRO
36
A
ILE
37
n
16
ILE
37
A
GLU
38
n
17
GLU
38
A
GLY
39
n
18
GLY
39
A
SER
40
n
19
SER
40
A
PHE
41
n
20
PHE
41
A
LYS
42
n
21
LYS
42
A
PRO
43
n
22
PRO
43
A
GLY
44
n
23
GLY
44
A
ASN
45
n
24
ASN
45
A
ILE
46
n
25
ILE
46
A
ASP
47
n
26
ASP
47
A
PRO
48
n
27
PRO
48
A
CYS
49
n
28
CYS
49
A
LEU
50
n
29
LEU
50
A
CYS
51
n
30
CYS
51
A
THR
52
n
31
THR
52
A
HIS
53
n
32
HIS
53
A
LEU
54
n
33
LEU
54
A
ILE
55
n
34
ILE
55
A
TYR
56
n
35
TYR
56
A
ALA
57
n
36
ALA
57
A
PHE
58
n
37
PHE
58
A
ALA
59
n
38
ALA
59
A
GLY
60
n
39
GLY
60
A
MET
61
n
40
MET
61
A
GLN
62
n
41
GLN
62
A
ASN
63
n
42
ASN
63
A
ASN
64
n
43
ASN
64
A
GLU
65
n
44
GLU
65
A
ILE
66
n
45
ILE
66
A
THR
67
n
46
THR
67
A
TYR
68
n
47
TYR
68
A
THR
69
n
48
THR
69
A
HIS
70
n
49
HIS
70
A
GLU
71
n
50
GLU
71
A
GLN
72
n
51
GLN
72
A
ASP
73
n
52
ASP
73
A
LEU
74
n
53
LEU
74
A
ARG
75
n
54
ARG
75
A
ASP
76
n
55
ASP
76
A
TYR
77
n
56
TYR
77
A
GLU
78
n
57
GLU
78
A
ALA
79
n
58
ALA
79
A
LEU
80
n
59
LEU
80
A
ASN
81
n
60
ASN
81
A
GLY
82
n
61
GLY
82
A
LEU
83
n
62
LEU
83
A
LYS
84
n
63
LYS
84
A
ASP
85
n
64
ASP
85
A
LYS
86
n
65
LYS
86
A
ASN
87
n
66
ASN
87
A
THR
88
n
67
THR
88
A
GLU
89
n
68
GLU
89
A
LEU
90
n
69
LEU
90
A
LYS
91
n
70
LYS
91
A
THR
92
n
71
THR
92
A
LEU
93
n
72
LEU
93
A
LEU
94
n
73
LEU
94
A
ALA
95
n
74
ALA
95
A
ILE
96
n
75
ILE
96
A
GLY
97
n
76
GLY
97
A
GLY
98
n
77
GLY
98
A
TRP
99
n
78
TRP
99
A
LYS
100
n
79
LYS
100
A
PHE
101
n
80
PHE
101
A
GLY
102
n
81
GLY
102
A
PRO
103
n
82
PRO
103
A
ALA
104
n
83
ALA
104
A
PRO
105
n
84
PRO
105
A
PHE
106
n
85
PHE
106
A
SER
107
n
86
SER
107
A
ALA
108
n
87
ALA
108
A
MET
109
n
88
MET
109
A
VAL
110
n
89
VAL
110
A
SER
111
n
90
SER
111
A
THR
112
n
91
THR
112
A
PRO
113
n
92
PRO
113
A
GLN
114
n
93
GLN
114
A
ASN
115
n
94
ASN
115
A
ARG
116
n
95
ARG
116
A
GLN
117
n
96
GLN
117
A
ILE
118
n
97
ILE
118
A
PHE
119
n
98
PHE
119
A
ILE
120
n
99
ILE
120
A
GLN
121
n
100
GLN
121
A
SER
122
n
101
SER
122
A
VAL
123
n
102
VAL
123
A
ILE
124
n
103
ILE
124
A
ARG
125
n
104
ARG
125
A
PHE
126
n
105
PHE
126
A
LEU
127
n
106
LEU
127
A
ARG
128
n
107
ARG
128
A
GLN
129
n
108
GLN
129
A
TYR
130
n
109
TYR
130
A
ASN
131
n
110
ASN
131
A
PHE
132
n
111
PHE
132
A
ASP
133
n
112
ASP
133
A
GLY
134
n
113
GLY
134
A
LEU
135
n
114
LEU
135
A
ASN
136
n
115
ASN
136
A
LEU
137
n
116
LEU
137
A
ASP
138
n
117
ASP
138
A
TRP
139
n
118
TRP
139
A
GLN
140
n
119
GLN
140
A
TYR
141
n
120
TYR
141
A
PRO
142
n
121
PRO
142
A
GLY
143
n
122
GLY
143
A
SER
144
n
123
SER
144
A
ARG
145
n
124
ARG
145
A
GLY
146
n
125
GLY
146
A
SER
147
n
126
SER
147
A
PRO
148
n
127
PRO
148
A
PRO
149
n
128
PRO
149
A
LYS
150
n
129
LYS
150
A
ASP
151
n
130
ASP
151
A
LYS
152
n
131
LYS
152
A
HIS
153
n
132
HIS
153
A
LEU
154
n
133
LEU
154
A
PHE
155
n
134
PHE
155
A
SER
156
n
135
SER
156
A
VAL
157
n
136
VAL
157
A
LEU
158
n
137
LEU
158
A
VAL
159
n
138
VAL
159
A
LYS
160
n
139
LYS
160
A
GLU
161
n
140
GLU
161
A
MET
162
n
141
MET
162
A
ARG
163
n
142
ARG
163
A
LYS
164
n
143
LYS
164
A
ALA
165
n
144
ALA
165
A
PHE
166
n
145
PHE
166
A
GLU
167
n
146
GLU
167
A
GLU
168
n
147
GLU
168
A
GLU
169
n
148
GLU
169
A
SER
170
n
149
SER
170
A
VAL
171
n
150
VAL
171
A
GLU
172
n
151
GLU
172
A
LYS
173
n
152
LYS
173
A
ASP
174
n
153
ASP
174
A
ILE
175
n
154
ILE
175
A
PRO
176
n
155
PRO
176
A
ARG
177
n
156
ARG
177
A
LEU
178
n
157
LEU
178
A
LEU
179
n
158
LEU
179
A
LEU
180
n
159
LEU
180
A
THR
181
n
160
THR
181
A
SER
182
n
161
SER
182
A
THR
183
n
162
THR
183
A
GLY
184
n
163
GLY
184
A
ALA
185
n
164
ALA
185
A
GLY
186
n
165
GLY
186
A
ILE
187
n
166
ILE
187
A
ILE
188
n
167
ILE
188
A
ASP
189
n
168
ASP
189
A
VAL
190
n
169
VAL
190
A
ILE
191
n
170
ILE
191
A
LYS
192
n
171
LYS
192
A
SER
193
n
172
SER
193
A
GLY
194
n
173
GLY
194
A
TYR
195
n
174
TYR
195
A
LYS
196
n
175
LYS
196
A
ILE
197
n
176
ILE
197
A
PRO
198
n
177
PRO
198
A
GLU
199
n
178
GLU
199
A
LEU
200
n
179
LEU
200
A
SER
201
n
180
SER
201
A
GLN
202
n
181
GLN
202
A
SER
203
n
182
SER
203
A
LEU
204
n
183
LEU
204
A
ASP
205
n
184
ASP
205
A
TYR
206
n
185
TYR
206
A
ILE
207
n
186
ILE
207
A
GLN
208
n
187
GLN
208
A
VAL
209
n
188
VAL
209
A
MET
210
n
189
MET
210
A
THR
211
n
190
THR
211
A
TYR
212
n
191
TYR
212
A
ASP
213
n
192
ASP
213
A
LEU
214
n
193
LEU
214
A
HIS
215
n
194
HIS
215
A
ASP
216
n
195
ASP
216
A
PRO
217
n
196
PRO
217
A
LYS
218
n
197
LYS
218
A
ASP
219
n
198
ASP
219
A
GLY
220
n
199
GLY
220
A
TYR
221
n
200
TYR
221
A
THR
222
n
201
THR
222
A
GLY
223
n
202
GLY
223
A
GLU
224
n
203
GLU
224
A
ASN
225
n
204
ASN
225
A
SER
226
n
205
SER
226
A
PRO
227
n
206
PRO
227
A
LEU
228
n
207
LEU
228
A
TYR
229
n
208
TYR
229
A
LYS
230
n
209
LYS
230
A
SER
231
n
210
SER
231
A
PRO
232
n
211
PRO
232
A
TYR
233
n
212
TYR
233
A
ASP
234
n
213
ASP
234
A
ILE
235
n
214
ILE
235
A
GLY
236
n
215
GLY
236
A
LYS
237
n
216
LYS
237
A
SER
238
n
217
SER
238
A
ALA
239
n
218
ALA
239
A
ASP
240
n
219
ASP
240
A
LEU
241
n
220
LEU
241
A
ASN
242
n
221
ASN
242
A
VAL
243
n
222
VAL
243
A
ASP
244
n
223
ASP
244
A
SER
245
n
224
SER
245
A
ILE
246
n
225
ILE
246
A
ILE
247
n
226
ILE
247
A
SER
248
n
227
SER
248
A
TYR
249
n
228
TYR
249
A
TRP
250
n
229
TRP
250
A
LYS
251
n
230
LYS
251
A
ASP
252
n
231
ASP
252
A
HIS
253
n
232
HIS
253
A
GLY
254
n
233
GLY
254
A
ALA
255
n
234
ALA
255
A
ALA
256
n
235
ALA
256
A
SER
257
n
236
SER
257
A
GLU
258
n
237
GLU
258
A
LYS
259
n
238
LYS
259
A
LEU
260
n
239
LEU
260
A
ILE
261
n
240
ILE
261
A
VAL
262
n
241
VAL
262
A
GLY
263
n
242
GLY
263
A
PHE
264
n
243
PHE
264
A
PRO
265
n
244
PRO
265
A
ALA
266
n
245
ALA
266
A
TYR
267
n
246
TYR
267
A
GLY
268
n
247
GLY
268
A
HIS
269
n
248
HIS
269
A
THR
270
n
249
THR
270
A
PHE
271
n
250
PHE
271
A
ILE
272
n
251
ILE
272
A
LEU
273
n
252
LEU
273
A
SER
274
n
253
SER
274
A
ASP
275
n
254
ASP
275
A
PRO
276
n
255
PRO
276
A
SER
277
n
256
SER
277
A
LYS
278
n
257
LYS
278
A
THR
279
n
258
THR
279
A
GLY
280
n
259
GLY
280
A
ILE
281
n
260
ILE
281
A
GLY
282
n
261
GLY
282
A
ALA
283
n
262
ALA
283
A
PRO
284
n
263
PRO
284
A
THR
285
n
264
THR
285
A
ILE
286
n
265
ILE
286
A
SER
287
n
266
SER
287
A
THR
288
n
267
THR
288
A
GLY
289
n
268
GLY
289
A
PRO
290
n
269
PRO
290
A
PRO
291
n
270
PRO
291
A
GLY
292
n
271
GLY
292
A
LYS
293
n
272
LYS
293
A
TYR
294
n
273
TYR
294
A
THR
295
n
274
THR
295
A
ASP
296
n
275
ASP
296
A
GLU
297
n
276
GLU
297
A
SER
298
n
277
SER
298
A
GLY
299
n
278
GLY
299
A
LEU
300
n
279
LEU
300
A
LEU
301
n
280
LEU
301
A
ALA
302
n
281
ALA
302
A
TYR
303
n
282
TYR
303
A
TYR
304
n
283
TYR
304
A
GLU
305
n
284
GLU
305
A
VAL
306
n
285
VAL
306
A
CYS
307
n
286
CYS
307
A
THR
308
n
287
THR
308
A
PHE
309
n
288
PHE
309
A
LEU
310
n
289
LEU
310
A
ASN
311
n
290
ASN
311
A
GLU
312
n
291
GLU
312
A
GLY
313
n
292
GLY
313
A
ALA
314
n
293
ALA
314
A
THR
315
n
294
THR
315
A
GLU
316
n
295
GLU
316
A
VAL
317
n
296
VAL
317
A
TRP
318
n
297
TRP
318
A
ASP
319
n
298
ASP
319
A
ALA
320
n
299
ALA
320
A
PRO
321
n
300
PRO
321
A
GLN
322
n
301
GLN
322
A
GLU
323
n
302
GLU
323
A
VAL
324
n
303
VAL
324
A
PRO
325
n
304
PRO
325
A
TYR
326
n
305
TYR
326
A
ALA
327
n
306
ALA
327
A
TYR
328
n
307
TYR
328
A
GLN
329
n
308
GLN
329
A
GLY
330
n
309
GLY
330
A
ASN
331
n
310
ASN
331
A
GLU
332
n
311
GLU
332
A
TRP
333
n
312
TRP
333
A
VAL
334
n
313
VAL
334
A
GLY
335
n
314
GLY
335
A
TYR
336
n
315
TYR
336
A
ASP
337
n
316
ASP
337
A
ASN
338
n
317
ASN
338
A
VAL
339
n
318
VAL
339
A
ARG
340
n
319
ARG
340
A
SER
341
n
320
SER
341
A
PHE
342
n
321
PHE
342
A
LYS
343
n
322
LYS
343
A
LEU
344
n
323
LEU
344
A
LYS
345
n
324
LYS
345
A
ALA
346
n
325
ALA
346
A
GLN
347
n
326
GLN
347
A
TRP
348
n
327
TRP
348
A
LEU
349
n
328
LEU
349
A
LYS
350
n
329
LYS
350
A
ASP
351
n
330
ASP
351
A
ASN
352
n
331
ASN
352
A
ASN
353
n
332
ASN
353
A
LEU
354
n
333
LEU
354
A
GLY
355
n
334
GLY
355
A
GLY
356
n
335
GLY
356
A
ALA
357
n
336
ALA
357
A
VAL
358
n
337
VAL
358
A
VAL
359
n
338
VAL
359
A
TRP
360
n
339
TRP
360
A
PRO
361
n
340
PRO
361
A
LEU
362
n
341
LEU
362
A
ASP
363
n
342
ASP
363
A
MET
364
n
343
MET
364
A
ASP
365
n
344
ASP
365
A
ASP
366
n
345
ASP
366
A
PHE
367
n
346
PHE
367
A
SER
368
n
347
SER
368
A
GLY
369
n
348
GLY
369
A
SER
370
n
349
SER
370
A
PHE
371
n
350
PHE
371
A
CYS
372
n
351
CYS
372
A
HIS
373
n
352
HIS
373
A
GLN
374
n
353
GLN
374
A
ARG
375
n
354
ARG
375
A
HIS
376
n
355
HIS
376
A
PHE
377
n
356
PHE
377
A
PRO
378
n
357
PRO
378
A
LEU
379
n
358
LEU
379
A
THR
380
n
359
THR
380
A
SER
381
n
360
SER
381
A
THR
382
n
361
THR
382
A
LEU
383
n
362
LEU
383
A
LYS
384
n
363
LYS
384
A
GLY
385
n
364
GLY
385
A
ASP
386
n
365
ASP
386
A
LEU
387
n
366
LEU
387
A
ASN
388
n
367
ASN
388
A
ILE
389
n
368
ILE
389
A
HIS
390
n
369
HIS
390
A
SER
391
n
370
SER
391
A
ALA
392
n
371
ALA
392
A
SER
393
n
372
SER
393
A
n
373
394
A
n
374
395
A
n
375
396
A
n
376
397
A
n
377
398
A
software_defined_assembly
PQS
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
N
MET
25
A
N
MET
4
A
O
ALA
357
A
O
ALA
336
A
N
GLY
356
A
N
GLY
335
A
O
LEU
260
A
O
LEU
239
A
N
ILE
261
A
N
ILE
240
A
O
ILE
207
A
O
ILE
186
A
N
GLN
208
A
N
GLN
187
A
O
SER
182
A
O
SER
161
A
N
THR
181
A
N
THR
160
A
O
LEU
135
A
O
LEU
114
A
N
ASN
136
A
N
ASN
115
A
O
LEU
94
A
O
LEU
73
A
N
LEU
93
A
N
LEU
72
A
O
LEU
54
A
O
LEU
33
A
N
ILE
286
A
N
ILE
265
A
O
ILE
272
A
O
ILE
251
A
N
GLY
268
A
N
GLY
247
A
O
LEU
301
A
O
LEU
280
A
N
ILE
286
A
N
ILE
265
A
O
ILE
272
A
O
ILE
251
A
N
PHE
271
A
N
PHE
250
A
O
TRP
333
A
O
TRP
312
A
N
VAL
334
A
N
VAL
313
A
O
ALA
327
A
O
ALA
306
A
N
TYR
328
A
N
TYR
307
A
O
THR
315
A
O
THR
294
1
A
CG
GLU
71
A
CG
GLU
50
1
Y
1
A
CD
GLU
71
A
CD
GLU
50
1
Y
1
A
OE1
GLU
71
A
OE1
GLU
50
1
Y
1
A
OE2
GLU
71
A
OE2
GLU
50
1
Y
1
A
CG
GLN
72
A
CG
GLN
51
1
Y
1
A
CD
GLN
72
A
CD
GLN
51
1
Y
1
A
OE1
GLN
72
A
OE1
GLN
51
1
Y
1
A
NE2
GLN
72
A
NE2
GLN
51
1
Y
1
A
CYS
394
A
CYS
373
1
Y
1
A
LYS
395
A
LYS
374
1
Y
1
A
GLY
396
A
GLY
375
1
Y
1
A
PRO
397
A
PRO
376
1
Y
1
A
TYR
398
A
TYR
377
1
Y
1
A
A
H1
H2
HOH
HOH
2125
2211
1.31
1
A
A
H
HD21
LYS
ASN
42
45
1.34
1
A
A
H
O
GLN
GLY
23
355
1.55
1
A
A
OH
O4
TYR
GCS
212
800
1.71
1
A
A
CH2
O3
TRP
GCS
360
800
1.91
1
A
A
CZ3
O3
TRP
GCS
360
800
2.00
1
9.73
1.50
119.30
129.03
A
A
A
C
N
CA
TYR
PRO
PRO
141
142
142
Y
1
-22.10
2.50
113.10
91.00
A
A
A
N
CA
C
GLY
GLY
GLY
355
355
355
N
1
A
A
N
CA
ASP
ASP
138
138
-0.201
0.020
1.459
1.258
N
1
A
ALA
57
-1.54
-97.75
1
A
LYS
84
-64.26
4.17
1
A
ALA
104
-28.74
-56.23
1
A
GLN
140
-67.20
91.46
1
A
TYR
141
69.89
96.12
1
A
ASP
174
72.89
65.87
1
A
PRO
217
-39.91
-20.75
1
A
PRO
232
-58.91
-0.96
1
A
ALA
266
-97.35
41.82
1
A
ASP
296
21.87
88.02
1
A
TYR
336
-135.90
-155.89
1
A
ASN
338
-127.76
-166.58
1
A
ASN
352
47.64
29.38
1
A
ASN
353
-78.36
45.50
1
A
LEU
354
-47.28
-171.50
1
A
ASP
366
-67.29
75.82
1
A
ARG
375
62.15
-175.49
1
A
PHE
377
44.81
72.66
PARHCSDX.PRO
TOPHCSDX.PRO
14.6
0.00
0.00
0.00
0.00
0.00
0.00
0.272
0.008
0.198
0.198
2.5
20.0
1154
11644
9.9
94.2
RANDOM
10000000.00
1
RESTRAINED
THROUGHOUT
2.0
MIRAS
0.36
0.27
3.5
0.38
0.32
2.5
20.0
214
3170
12
0
2944
0.008
1.4
27.8
0.71
1.8
1.5
1.3
2.00
1.34
2.00
0.52
2.50
0.328
0.027
0.244
2.66
147
1568
6
8.6
89.4
21.2
2.500
20.000
1E9L
11644
2.000
0.03900
1
15.3000
3.690
94.2
0.21000
2.50
2.60
5.150
1
2.80
89.4
refinement
X-PLOR
3.851
data reduction
DENZO
data scaling
SCALEPACK
phasing
CCP4
YM1 SECRETORY PROTEIN
The crystal structure of novel mammalian lectin Ym1 suggests a saccharide binding site
1
N
N
2
N
N
3
N
N
A
THR
29
A
THR
8
HELX_P
A
LYS
33
A
LYS
12
5
1
5
A
PRO
36
A
PRO
15
HELX_P
A
SER
40
A
SER
19
5
2
5
A
LYS
42
A
LYS
21
HELX_P
A
ILE
46
A
ILE
25
5
3
5
A
GLN
72
A
GLN
51
HELX_P
A
GLY
82
A
GLY
61
1
4
11
A
LEU
83
A
LEU
62
HELX_P
A
LYS
86
A
LYS
65
5
5
4
A
PRO
103
A
PRO
82
HELX_P
A
SER
111
A
SER
90
1
6
9
A
THR
112
A
THR
91
HELX_P
A
TYR
130
A
TYR
109
1
7
19
A
PRO
149
A
PRO
128
HELX_P
A
LYS
173
A
LYS
152
1
8
25
A
ILE
187
A
ILE
166
HELX_P
A
TYR
195
A
TYR
174
1
9
9
A
LYS
196
A
LYS
175
HELX_P
A
LEU
204
A
LEU
183
1
10
9
A
ASP
216
A
ASP
195
HELX_P
A
GLY
220
A
GLY
199
5
11
5
A
ILE
235
A
ILE
214
HELX_P
A
LEU
241
A
LEU
220
5
12
7
A
ASN
242
A
ASN
221
HELX_P
A
HIS
253
A
HIS
232
1
13
12
A
ALA
256
A
ALA
235
HELX_P
A
GLU
258
A
GLU
237
5
14
3
A
TYR
303
A
TYR
282
HELX_P
A
GLU
312
A
GLU
291
1
15
10
A
ASN
338
A
ASN
317
HELX_P
A
LEU
349
A
LEU
328
1
16
12
A
PRO
361
A
PRO
340
HELX_P
A
ASP
365
A
ASP
344
5
17
5
A
PHE
377
A
PHE
356
HELX_P
A
LEU
387
A
LEU
366
1
18
11
disulf
2.021
A
CYS
26
A
SG
CYS
5
1_555
A
CYS
51
A
SG
CYS
30
1_555
disulf
2.024
A
CYS
307
A
SG
CYS
286
1_555
A
CYS
372
A
SG
CYS
351
1_555
MACROPHAGE SECRETORY PROTEIN
MACROPHAGE SECRETORY PROTEIN, INFLAMMATION, LECTIN, INDUCIBLE, SECRETORY
A
TRP
360
A
TRP
339
1
A
PRO
361
A
PRO
340
-0.21
O35744
UNP
1
O35744
22
399
1E9L
22
398
O35744
A
1
1
377
8
3
5
parallel
parallel
parallel
parallel
parallel
parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
GLN
23
A
GLN
2
A
TYR
28
A
TYR
7
A
GLY
356
A
GLY
335
A
TRP
360
A
TRP
339
A
LEU
260
A
LEU
239
A
PRO
265
A
PRO
244
A
TYR
206
A
TYR
185
A
VAL
209
A
VAL
188
A
LEU
179
A
LEU
158
A
GLY
184
A
GLY
163
A
GLY
134
A
GLY
113
A
TRP
139
A
TRP
118
A
LYS
91
A
LYS
70
A
GLY
98
A
GLY
77
A
HIS
53
A
HIS
32
A
MET
61
A
MET
40
A
THR
285
A
THR
264
A
THR
288
A
THR
267
A
TYR
267
A
TYR
246
A
LEU
273
A
LEU
252
A
LEU
300
A
LEU
279
A
ALA
302
A
ALA
281
A
THR
285
A
THR
264
A
THR
288
A
THR
267
A
TYR
267
A
TYR
246
A
LEU
273
A
LEU
252
A
GLU
332
A
GLU
311
A
GLY
335
A
GLY
314
A
VAL
324
A
VAL
303
A
GLN
329
A
GLN
308
A
THR
315
A
THR
294
A
ASP
319
A
ASP
298
4
P 1 21 1