0.017182
0.000000
0.000000
0.000000
0.016453
0.000000
0.000000
0.000000
0.030553
0.00000
0.00000
0.00000
Muraki, M.
Harata, K.
Sugita, N.
Sato, K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
58.20
60.78
32.73
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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
C8 H15 N O6
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE
D-saccharide, beta 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
Biochemistry
BICHAW
0033
0006-2960
39
292
299
10.1021/bi991402q
10630988
Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling.
2000
US
Biochemistry
BICHAW
0033
0006-2960
38
540
548
10.1021/bi981779g
Dual Affinity Labeling of the Active Site of Human Lysozyme with an N-Acetyllactosamine Derivative: First Ligand Assisted Recognition of the Second Ligand
1999
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
54
834
843
10.1107/S090744499800122X
X-ray Structure of Human Lysozyme Labelled with 2',3'-Epoxypropyl b-Glycoside of Man-b1,4-GlcNAc. Structural Change and Recognition Specificity at Subsite B
1998
US
Biochemistry
BICHAW
0033
0006-2960
35
13562
13567
10.1021/bi9613180
Origin of Carbohydrate Recognition Specificity of Human Lysozyme Revealed by Affinity Labeling
1996
US
Biochemistry
BICHAW
0033
0006-2960
31
9212
9219
Dissection of the Functional Role of Structural Elements of Tyrosine-63 in the Catalytic Action of Human Lysozyme
1992
10.2210/pdb1d6p/pdb
pdb_00001d6p
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
288.0
1
DIFFRACTOMETER
1999-05-10
ENRAF-NONIUS FAST
SINGLE WAVELENGTH
M
x-ray
1
1.5148
1.0
1.5148
ROTATING ANODE
ENRAF-NONIUS FR571
14670.676
LYSOZYME
3.2.1.17
Y63L
1
man
polymer
424.401
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
1
man
branched
92.094
GLYCEROL
1
syn
non-polymer
18.015
water
43
nat
water
no
no
KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRLWCNDGKTPGAVNACHLS
CSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV
KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRLWCNDGKTPGAVNACHLS
CSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV
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
sample
9606
Homo sapiens
1
1.97
37.65
VAPOR DIFFUSION, SITTING DROP
4.5
5M NH4NO3 IN 10 MM NAOAC(PH 4.5), VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
298.0
software
diffrn_detector
atom_site
chem_comp
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
struct_asym
struct_conn
struct_site
struct_site_gen
chem_comp
database_2
struct_ref_seq_dif
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Non-polymer description
Version format compliance
Refinement description
Data collection
Atomic model
Data collection
Derived calculations
Structure summary
Database references
Structure summary
1
0
2000-01-21
1
1
2007-10-16
1
2
2011-07-13
1
3
2017-10-04
1
4
2018-04-18
2
0
2020-07-29
2
1
2021-11-03
_software.name
_diffrn_detector.detector
_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_seq_id
_atom_site.label_asym_id
_chem_comp.name
_chem_comp.type
_entity.formula_weight
_entity.pdbx_description
_entity.pdbx_number_of_molecules
_entity.type
_pdbx_struct_assembly_gen.asym_id_list
_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.ptnr1_label_seq_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
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
NAG
132
n
B
NAG
1
NAG
131
n
B
NAG
2
DGlcpNAcb
N-acetyl-b-D-glucopyranosamine
b-D-GlcpNAc
GlcNAc
HUMAN LYSOZYME (WILD TYPE) LABELLED WITH 2',3'-EPOXYPROPYL GLYCOSIDE OF N,N'-DIACETYL CHITOBIOSE
HUMAN LYSOZYME D102E MUTANT
RCSB
Y
RCSB
1999-10-15
REL
REL
oligosaccharide
DGlcpNAcb1-4DGlcpNAcb1-ROH
2
GMML
1.0
Glycam Condensed Sequence
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1
2
PDB2Glycan
1.1.0
WURCS
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}
2
PDB-CARE
LINUCS
C1
O4
NAG
NAG
2
1
2
O1
HO4
sing
n
n
GOL
GLYCEROL
HOH
water
GOL
133
3
GOL
GOL
133
A
HOH
134
4
HOH
HOH
134
A
HOH
135
4
HOH
HOH
135
A
HOH
136
4
HOH
HOH
136
A
HOH
137
4
HOH
HOH
137
A
HOH
138
4
HOH
HOH
138
A
HOH
139
4
HOH
HOH
139
A
HOH
140
4
HOH
HOH
140
A
HOH
141
4
HOH
HOH
141
A
HOH
142
4
HOH
HOH
142
A
HOH
143
4
HOH
HOH
143
A
HOH
144
4
HOH
HOH
144
A
HOH
145
4
HOH
HOH
145
A
HOH
146
4
HOH
HOH
146
A
HOH
147
4
HOH
HOH
147
A
HOH
148
4
HOH
HOH
148
A
HOH
149
4
HOH
HOH
149
A
HOH
150
4
HOH
HOH
150
A
HOH
151
4
HOH
HOH
151
A
HOH
152
4
HOH
HOH
152
A
HOH
153
4
HOH
HOH
153
A
HOH
154
4
HOH
HOH
154
A
HOH
155
4
HOH
HOH
155
A
HOH
156
4
HOH
HOH
156
A
HOH
157
4
HOH
HOH
157
A
HOH
158
4
HOH
HOH
158
A
HOH
159
4
HOH
HOH
159
A
HOH
160
4
HOH
HOH
160
A
HOH
161
4
HOH
HOH
161
A
HOH
162
4
HOH
HOH
162
A
HOH
163
4
HOH
HOH
163
A
HOH
164
4
HOH
HOH
164
A
HOH
165
4
HOH
HOH
165
A
HOH
166
4
HOH
HOH
166
A
HOH
167
4
HOH
HOH
167
A
HOH
168
4
HOH
HOH
168
A
HOH
169
4
HOH
HOH
169
A
HOH
170
4
HOH
HOH
170
A
HOH
171
4
HOH
HOH
171
A
HOH
172
4
HOH
HOH
172
A
HOH
173
4
HOH
HOH
173
A
HOH
174
4
HOH
HOH
174
A
HOH
175
4
HOH
HOH
175
A
HOH
176
4
HOH
HOH
176
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
LEU
63
n
63
LEU
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
TRP
109
n
109
TRP
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
N
ASN
46
A
N
ASN
46
A
O
SER
51
A
O
SER
51
A
O
TYR
54
A
O
TYR
54
A
N
ILE
59
A
N
ILE
59
A
N
ASN
66
A
N
ASN
66
A
O
LEU
79
A
O
LEU
79
1
17.18
2.30
115.30
132.48
A
A
A
CA
CB
CG
LEU
LEU
LEU
63
63
63
N
1
9.36
1.50
119.30
128.66
A
A
A
C
N
CA
THR
PRO
PRO
70
71
71
Y
1
A
GLN
58
36.14
72.47
98.3 % COMPLETENESS OF DATA
0.216
0.181
0.181
2.23
8.0
3865
RANDOM
1
2
2.23
8.0
43
1101
33
0
1025
0.011
1.87
2.23
22.27
1D6P
52931
40267
0.0
0.1
1
3.4
0.293
2.23
2.32
1
data collection
MADNESS
data reduction
MERGEF
(BY K.HARATA)
model building
X-PLOR
refinement
X-PLOR
3.1
data reduction
MADNESS
data scaling
MERGEF
(K.HARATA)
phasing
X-PLOR
HUMAN LYSOZYME L63 MUTANT LABELLED WITH 2',3'-EPOXYPROPYL N,N'-DIACETYLCHITOBIOSE
1
N
N
2
N
N
3
N
N
4
N
N
A
GLU
4
A
GLU
4
HELX_P
A
LEU
15
A
LEU
15
1
1
12
A
SER
24
A
SER
24
HELX_P
A
GLY
37
A
GLY
37
1
2
14
A
SER
82
A
SER
82
HELX_P
A
LEU
85
A
LEU
85
5
3
4
A
ILE
89
A
ILE
89
HELX_P
A
ASP
102
A
ASP
102
1
4
14
A
GLN
104
A
GLN
104
HELX_P
A
ALA
108
A
ALA
108
5
5
5
A
TRP
109
A
TRP
109
HELX_P
A
CYS
116
A
CYS
116
1
6
8
A
VAL
121
A
VAL
121
HELX_P
A
VAL
125
A
VAL
125
5
7
5
disulf
2.034
A
CYS
6
A
SG
CYS
6
1_555
A
CYS
128
A
SG
CYS
128
1_555
disulf
2.023
A
CYS
30
A
SG
CYS
30
1_555
A
CYS
116
A
SG
CYS
116
1_555
disulf
2.027
A
CYS
65
A
SG
CYS
65
1_555
A
CYS
81
A
SG
CYS
81
1_555
disulf
2.023
A
CYS
77
A
SG
CYS
77
1_555
A
CYS
95
A
SG
CYS
95
1_555
covale
1.473
none
A
ASP
53
A
OD1
ASP
53
1_555
A
GOL
133
C
C3
GOL
1_555
covale
1.363
one
A
GOL
133
C
O1
GOL
1_555
B
NAG
1
B
C1
NAG
1_555
covale
1.370
both
B
NAG
1
B
O4
NAG
1_555
B
NAG
2
B
C1
NAG
1_555
HYDROLASE
LYSOZYME, MURAMIDASE, HYDROLASE (O-GLYCOSYL), SITE-DIRECTED MUTAGENESIS, N, N'-DIACETYLCHITOBIOSE, AFFINITY LABELING, HYDROLASE
LYSC_HUMAN
UNP
1
P00695
19
148
1D6P
1
130
P00695
A
1
1
130
1
TYR
engineered mutation
LEU
63
1D6P
A
P00695
UNP
81
63
3
2
anti-parallel
anti-parallel
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
A
ILE
59
A
ILE
59
A
ASN
60
A
ASN
60
A
CYS
65
A
CYS
65
A
ASN
66
A
ASN
66
A
LEU
79
A
LEU
79
A
SER
80
A
SER
80
19
P 21 21 21