0.017479
0.000000
0.000000
0.000000
0.016343
0.000000
0.000000
0.000000
0.030312
0.00000
0.00000
0.00000
Muraki, M.
Harata, K.
Goda, S.
Nagahora, H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
57.210
61.190
32.990
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
N O3 -1
62.005
NITRATE ION
non-polymer
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
Protein Sci.
PRCIEI
0795
0961-8368
6
473
476
9041653
Importance of van der Waals contact between Glu 35 and Trp 109 to the catalytic action of human lysozyme.
1997
NE
Biochim.Biophys.Acta
BBACAQ
0113
0006-3002
916
66
The Roles of Conserved Aromatic Amino-Acid Residues in the Active Site of Human Lysozyme: A Site-Specific Mutagenesis Study
1987
10.2210/pdb1jkd/pdb
pdb_00001jkd
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
DIFFRACTOMETER
ENRAF-NONIUS FAST
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
ENRAF-NONIUS FR571
14605.561
LYSOZYME
3.2.1.17
W109A
1
man
polymer
62.005
NITRATE ION
2
syn
non-polymer
18.015
water
76
nat
water
no
no
KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLS
CSALLQDNIADAVACAKRVVRDPQGIRAAVAWRNRCQNRDVRQYVQGCGV
KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLS
CSALLQDNIADAVACAKRVVRDPQGIRAAVAWRNRCQNRDVRQYVQGCGV
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
human
Homo
baker's yeast
Saccharomyces
sample
A SYNTHETIC GENE OF HUMAN LYSO
9606
Homo sapiens
A SYNTHETIC GENE OF HUMAN LYSOZYME WITH A MUTATION OF W109A
4932
Saccharomyces cerevisiae
KSC22-1C
YEP
YEPHLYSIG (ALA109)
1.96
37.
4.5
5 M NH4NO3 IN 20 MM NA ACETATE (PH4.5)
diffrn_detector
pdbx_database_status
database_2
struct_ref_seq_dif
struct_site
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Data collection
Other
Database references
Derived calculations
Refinement description
1
0
1997-05-15
1
1
2008-03-03
1
2
2011-07-13
1
3
2018-04-18
1
4
2021-11-03
1
5
2023-08-09
_diffrn_detector.detector
_pdbx_database_status.process_site
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
BNL
1996-11-13
REL
REL
NO3
NITRATE ION
HOH
water
1LZ1
PDB ENTRY 1LZ1
PDB
experimental model
NO3
1
2
NO3
NO3
131
A
NO3
2
2
NO3
NO3
132
A
HOH
1
3
HOH
HOH
133
A
HOH
2
3
HOH
HOH
134
A
HOH
3
3
HOH
HOH
135
A
HOH
4
3
HOH
HOH
136
A
HOH
5
3
HOH
HOH
137
A
HOH
6
3
HOH
HOH
138
A
HOH
7
3
HOH
HOH
139
A
HOH
8
3
HOH
HOH
140
A
HOH
9
3
HOH
HOH
141
A
HOH
10
3
HOH
HOH
142
A
HOH
11
3
HOH
HOH
143
A
HOH
12
3
HOH
HOH
144
A
HOH
13
3
HOH
HOH
145
A
HOH
14
3
HOH
HOH
146
A
HOH
15
3
HOH
HOH
147
A
HOH
16
3
HOH
HOH
148
A
HOH
17
3
HOH
HOH
149
A
HOH
18
3
HOH
HOH
150
A
HOH
19
3
HOH
HOH
151
A
HOH
20
3
HOH
HOH
152
A
HOH
21
3
HOH
HOH
153
A
HOH
22
3
HOH
HOH
154
A
HOH
23
3
HOH
HOH
155
A
HOH
24
3
HOH
HOH
156
A
HOH
25
3
HOH
HOH
157
A
HOH
26
3
HOH
HOH
158
A
HOH
27
3
HOH
HOH
159
A
HOH
28
3
HOH
HOH
160
A
HOH
29
3
HOH
HOH
161
A
HOH
30
3
HOH
HOH
162
A
HOH
31
3
HOH
HOH
163
A
HOH
32
3
HOH
HOH
164
A
HOH
33
3
HOH
HOH
165
A
HOH
34
3
HOH
HOH
166
A
HOH
35
3
HOH
HOH
167
A
HOH
36
3
HOH
HOH
168
A
HOH
37
3
HOH
HOH
169
A
HOH
38
3
HOH
HOH
170
A
HOH
39
3
HOH
HOH
171
A
HOH
40
3
HOH
HOH
172
A
HOH
41
3
HOH
HOH
173
A
HOH
42
3
HOH
HOH
174
A
HOH
43
3
HOH
HOH
175
A
HOH
44
3
HOH
HOH
176
A
HOH
45
3
HOH
HOH
177
A
HOH
46
3
HOH
HOH
178
A
HOH
47
3
HOH
HOH
179
A
HOH
48
3
HOH
HOH
180
A
HOH
49
3
HOH
HOH
181
A
HOH
50
3
HOH
HOH
182
A
HOH
51
3
HOH
HOH
183
A
HOH
52
3
HOH
HOH
184
A
HOH
53
3
HOH
HOH
185
A
HOH
54
3
HOH
HOH
186
A
HOH
55
3
HOH
HOH
187
A
HOH
56
3
HOH
HOH
188
A
HOH
57
3
HOH
HOH
189
A
HOH
58
3
HOH
HOH
190
A
HOH
59
3
HOH
HOH
191
A
HOH
60
3
HOH
HOH
192
A
HOH
61
3
HOH
HOH
193
A
HOH
62
3
HOH
HOH
194
A
HOH
63
3
HOH
HOH
195
A
HOH
64
3
HOH
HOH
196
A
HOH
65
3
HOH
HOH
197
A
HOH
66
3
HOH
HOH
198
A
HOH
67
3
HOH
HOH
199
A
HOH
68
3
HOH
HOH
200
A
HOH
69
3
HOH
HOH
201
A
HOH
70
3
HOH
HOH
202
A
HOH
71
3
HOH
HOH
203
A
HOH
72
3
HOH
HOH
204
A
HOH
73
3
HOH
HOH
205
A
HOH
74
3
HOH
HOH
206
A
HOH
75
3
HOH
HOH
207
A
HOH
76
3
HOH
HOH
208
A
LYS
1
n
1
LYS
1
A
VAL
2
n
2
VAL
2
A
PHE
3
n
3
PHE
3
A
GLU
4
n
4
GLU
4
A
ARG
5
n
5
ARG
5
A
CYS
6
n
6
CYS
6
A
GLU
7
n
7
GLU
7
A
LEU
8
n
8
LEU
8
A
ALA
9
n
9
ALA
9
A
ARG
10
n
10
ARG
10
A
THR
11
n
11
THR
11
A
LEU
12
n
12
LEU
12
A
LYS
13
n
13
LYS
13
A
ARG
14
n
14
ARG
14
A
LEU
15
n
15
LEU
15
A
GLY
16
n
16
GLY
16
A
MET
17
n
17
MET
17
A
ASP
18
n
18
ASP
18
A
GLY
19
n
19
GLY
19
A
TYR
20
n
20
TYR
20
A
ARG
21
n
21
ARG
21
A
GLY
22
n
22
GLY
22
A
ILE
23
n
23
ILE
23
A
SER
24
n
24
SER
24
A
LEU
25
n
25
LEU
25
A
ALA
26
n
26
ALA
26
A
ASN
27
n
27
ASN
27
A
TRP
28
n
28
TRP
28
A
MET
29
n
29
MET
29
A
CYS
30
n
30
CYS
30
A
LEU
31
n
31
LEU
31
A
ALA
32
n
32
ALA
32
A
LYS
33
n
33
LYS
33
A
TRP
34
n
34
TRP
34
A
GLU
35
n
35
GLU
35
A
SER
36
n
36
SER
36
A
GLY
37
n
37
GLY
37
A
TYR
38
n
38
TYR
38
A
ASN
39
n
39
ASN
39
A
THR
40
n
40
THR
40
A
ARG
41
n
41
ARG
41
A
ALA
42
n
42
ALA
42
A
THR
43
n
43
THR
43
A
ASN
44
n
44
ASN
44
A
TYR
45
n
45
TYR
45
A
ASN
46
n
46
ASN
46
A
ALA
47
n
47
ALA
47
A
GLY
48
n
48
GLY
48
A
ASP
49
n
49
ASP
49
A
ARG
50
n
50
ARG
50
A
SER
51
n
51
SER
51
A
THR
52
n
52
THR
52
A
ASP
53
n
53
ASP
53
A
TYR
54
n
54
TYR
54
A
GLY
55
n
55
GLY
55
A
ILE
56
n
56
ILE
56
A
PHE
57
n
57
PHE
57
A
GLN
58
n
58
GLN
58
A
ILE
59
n
59
ILE
59
A
ASN
60
n
60
ASN
60
A
SER
61
n
61
SER
61
A
ARG
62
n
62
ARG
62
A
TYR
63
n
63
TYR
63
A
TRP
64
n
64
TRP
64
A
CYS
65
n
65
CYS
65
A
ASN
66
n
66
ASN
66
A
ASP
67
n
67
ASP
67
A
GLY
68
n
68
GLY
68
A
LYS
69
n
69
LYS
69
A
THR
70
n
70
THR
70
A
PRO
71
n
71
PRO
71
A
GLY
72
n
72
GLY
72
A
ALA
73
n
73
ALA
73
A
VAL
74
n
74
VAL
74
A
ASN
75
n
75
ASN
75
A
ALA
76
n
76
ALA
76
A
CYS
77
n
77
CYS
77
A
HIS
78
n
78
HIS
78
A
LEU
79
n
79
LEU
79
A
SER
80
n
80
SER
80
A
CYS
81
n
81
CYS
81
A
SER
82
n
82
SER
82
A
ALA
83
n
83
ALA
83
A
LEU
84
n
84
LEU
84
A
LEU
85
n
85
LEU
85
A
GLN
86
n
86
GLN
86
A
ASP
87
n
87
ASP
87
A
ASN
88
n
88
ASN
88
A
ILE
89
n
89
ILE
89
A
ALA
90
n
90
ALA
90
A
ASP
91
n
91
ASP
91
A
ALA
92
n
92
ALA
92
A
VAL
93
n
93
VAL
93
A
ALA
94
n
94
ALA
94
A
CYS
95
n
95
CYS
95
A
ALA
96
n
96
ALA
96
A
LYS
97
n
97
LYS
97
A
ARG
98
n
98
ARG
98
A
VAL
99
n
99
VAL
99
A
VAL
100
n
100
VAL
100
A
ARG
101
n
101
ARG
101
A
ASP
102
n
102
ASP
102
A
PRO
103
n
103
PRO
103
A
GLN
104
n
104
GLN
104
A
GLY
105
n
105
GLY
105
A
ILE
106
n
106
ILE
106
A
ARG
107
n
107
ARG
107
A
ALA
108
n
108
ALA
108
A
ALA
109
n
109
ALA
109
A
VAL
110
n
110
VAL
110
A
ALA
111
n
111
ALA
111
A
TRP
112
n
112
TRP
112
A
ARG
113
n
113
ARG
113
A
ASN
114
n
114
ASN
114
A
ARG
115
n
115
ARG
115
A
CYS
116
n
116
CYS
116
A
GLN
117
n
117
GLN
117
A
ASN
118
n
118
ASN
118
A
ARG
119
n
119
ARG
119
A
ASP
120
n
120
ASP
120
A
VAL
121
n
121
VAL
121
A
ARG
122
n
122
ARG
122
A
GLN
123
n
123
GLN
123
A
TYR
124
n
124
TYR
124
A
VAL
125
n
125
VAL
125
A
GLN
126
n
126
GLN
126
A
GLY
127
n
127
GLY
127
A
CYS
128
n
128
CYS
128
A
GLY
129
n
129
GLY
129
A
VAL
130
n
130
VAL
130
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
ASN
44
A
O
ASN
44
A
N
ASP
53
A
N
ASP
53
19.04
0.245
0.174
0.174
1.80
8.0
10886
10.
1
3.
MOLECULAR REPLACEMENT
PDB ENTRY 1LZ1
0.2
1.80
8.0
76
1104
8
0
1020
0.010
1.483
24.34
1.341
1.61
14.5
1JKD
13422
0.0
0.056
1
3.1
86.6
data collection
MADNES
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
data reduction
MADNES
phasing
X-PLOR
3.1
HUMAN LYSOZYME MUTANT WITH TRP 109 REPLACED BY ALA
1
N
N
2
N
N
2
N
N
3
N
N
A
ARG
5
A
ARG
5
HELX_P
A
ARG
14
A
ARG
14
1
1
10
A
TYR
20
A
TYR
20
HELX_P
A
GLY
22
A
GLY
22
5
2
3
A
LEU
25
A
LEU
25
HELX_P
A
SER
36
A
SER
36
1
3
12
A
CYS
81
A
CYS
81
HELX_P
A
LEU
85
A
LEU
85
5
4
5
A
ALA
90
A
ALA
90
HELX_P
A
ARG
101
A
ARG
101
1
5
12
A
GLY
105
A
GLY
105
HELX_P
A
ALA
108
A
ALA
108
5
6
4
A
VAL
110
A
VAL
110
HELX_P
A
ARG
115
A
ARG
115
1
7
6
A
ARG
122
A
ARG
122
HELX_P
A
TYR
124
A
TYR
124
5
8
3
disulf
2.038
A
CYS
6
A
SG
CYS
6
1_555
A
CYS
128
A
SG
CYS
128
1_555
disulf
2.013
A
CYS
30
A
SG
CYS
30
1_555
A
CYS
116
A
SG
CYS
116
1_555
disulf
2.055
A
CYS
65
A
SG
CYS
65
1_555
A
CYS
81
A
SG
CYS
81
1_555
disulf
2.016
A
CYS
77
A
SG
CYS
77
1_555
A
CYS
95
A
SG
CYS
95
1_555
LYSOZYME
HYDROLASE, MURAMIDASE, HYDROLASE (O-GLYCOSYL), GLYCOSIDASE, LYSOZYME
LYSC_HUMAN
UNP
1
1
P61626
MKALIVLGLVLLSVTVQGKVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSR
YWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV
19
148
1JKD
1
130
P61626
A
1
1
130
1
TRP
engineered mutation
ALA
109
1JKD
A
P61626
UNP
127
109
2
anti-parallel
A
THR
43
A
THR
43
A
ASN
46
A
ASN
46
A
SER
51
A
SER
51
A
TYR
54
A
TYR
54
BINDING SITE FOR RESIDUE NO3 A 131
A
NO3
131
Software
5
BINDING SITE FOR RESIDUE NO3 A 132
A
NO3
132
Software
7
A
GLU
4
A
GLU
4
5
1_555
A
CYS
6
A
CYS
6
5
1_555
A
GLU
7
A
GLU
7
5
1_555
A
ARG
14
A
ARG
14
5
2_564
A
HOH
170
D
HOH
5
1_555
A
ASN
27
A
ASN
27
7
1_555
A
ASN
66
A
ASN
66
7
4_557
A
ASN
75
A
ASN
75
7
4_557
A
LEU
79
A
LEU
79
7
4_557
A
HOH
135
D
HOH
7
4_557
A
HOH
166
D
HOH
7
1_555
A
HOH
194
D
HOH
7
1_555
19
P 21 21 21