PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
1M54
Biol. Unit 3
Info
Asym.Unit (340 KB)
Biol.Unit 1 (114 KB)
Biol.Unit 2 (113 KB)
Biol.Unit 3 (114 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CYSTATHIONINE-BETA SYNTHASE: REDUCED VICINAL THIOLS
Authors
:
S. Taoka, B. W. Lepore, O. Kabil, S. Ojha, D. Ringe, R. Banerjee
Date
:
08 Jul 02 (Deposition) - 14 Aug 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Keywords
:
Plp Protein Fold Type Ii (Tryptophan Synthase), Plp And Heme Bound To Protein, Reduced Vicinal Cysteines, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Taoka, B. W. Lepore, O. Kabil, S. Ojha, D. Ringe, R. Banerjee
Human Cystathionine Beta-Synthase Is A Heme Sensor Protein. Evidence That The Redox Sensor Is Heme And Not The Vicinal Cysteines In The Cxxc Motif Seen In The Crystal Structure O The Truncated Enzyme
Biochemistry V. 41 10454 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
1b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
1c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
1d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
1e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
1f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
2a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
2b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
2c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
2d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
2e: PYRIDOXAL-5'-PHOSPHATE (PLPe)
2f: PYRIDOXAL-5'-PHOSPHATE (PLPf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC9 (SOFTWARE)
5: BC2 (SOFTWARE)
6: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
LYS E:119 , ASN E:149 , SER E:254 , VAL E:255 , GLY E:256 , THR E:257 , GLY E:258 , GLY E:259 , THR E:260 , GLU E:304 , GLY E:305 , ILE E:306 , SER E:349 , PRO E:375 , TYR E:381 , HOH E:1523
BINDING SITE FOR RESIDUE PLP E 1510
2
AC6
SOFTWARE
LYS F:119 , ASN F:149 , SER F:254 , VAL F:255 , GLY F:256 , THR F:257 , GLY F:258 , GLY F:259 , THR F:260 , GLY F:305 , ILE F:306 , SER F:349 , PRO F:375 , ASP F:376 , TYR F:381
BINDING SITE FOR RESIDUE PLP F 1610
3
AC7
SOFTWARE
ARG A:51 , CYS A:52 , THR A:53 , TRP A:54 , ARG A:58 , GLU A:62 , SER A:63 , PRO A:64 , HIS A:65 , ALA A:226 , PRO A:229 , LEU A:230 , TYR A:233 , ARG A:266 , THR F:53 , ARG F:58
BINDING SITE FOR RESIDUE HEM A 1120
4
AC9
SOFTWARE
SER C:50 , ARG C:51 , CYS C:52 , THR C:53 , ARG C:58 , GLU C:62 , PRO C:64 , HIS C:65 , ALA C:226 , PRO C:229 , LEU C:230 , TYR C:233 , ARG C:266 , ARG E:58
BINDING SITE FOR RESIDUE HEM C 1320
5
BC2
SOFTWARE
THR C:53 , ARG C:58 , SER E:50 , ARG E:51 , CYS E:52 , TRP E:54 , GLU E:62 , SER E:63 , PRO E:64 , HIS E:65 , ALA E:226 , PRO E:229 , LEU E:230 , TYR E:233 , ARG E:266 , HOH E:1535
BINDING SITE FOR RESIDUE HEM E 1520
6
BC3
SOFTWARE
ARG A:58 , ARG F:51 , CYS F:52 , THR F:53 , TRP F:54 , ARG F:58 , GLU F:62 , SER F:63 , PRO F:64 , HIS F:65 , ARG F:224 , ALA F:226 , PRO F:229 , LEU F:230 , ARG F:266 , VAL F:314
BINDING SITE FOR RESIDUE HEM F 1620
[
close Site info
]
SAPs(SNPs)/Variants
(87, 172)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_008049 (P49L, chain E/F, )
02: VAR_008050 (R58W, chain E/F, )
03: VAR_021790 (H65R, chain E/F, )
04: VAR_046922 (A69P, chain E/F, )
05: VAR_002171 (P78R, chain E/F, )
06: VAR_008051 (G85R, chain E/F, )
07: VAR_002172 (P88S, chain E/F, )
08: VAR_021791 (L101P, chain E/F, )
09: VAR_002173 (K102N, chain E/F, )
10: VAR_008052 (K102Q, chain E/F, )
11: VAR_021792 (C109R, chain E/F, )
12: VAR_002174 (A114V, chain E/F, )
13: VAR_008053 (G116R, chain E/F, )
14: VAR_008054 (R121C, chain E/F, )
15: VAR_008055 (R121H, chain E/F, )
16: VAR_008056 (R121L, chain E/F, )
17: VAR_046923 (R125P, chain E/F, )
18: VAR_002175 (R125Q, chain E/F, )
19: VAR_008057 (R125W, chain E/F, )
20: VAR_008058 (M126V, chain E/F, )
21: VAR_008059 (E128D, chain E/F, )
22: VAR_002176 (E131D, chain E/F, )
23: VAR_008060 (G139R, chain E/F, )
24: VAR_021793 (I143M, chain E/F, )
25: VAR_002177 (E144K, chain E/F, )
26: VAR_002178 (P145L, chain E/F, )
27: VAR_008061 (G148R, chain E/F, )
28: VAR_008062 (G151R, chain E/F, )
29: VAR_008064 (I152M, chain E/F, )
30: VAR_046924 (L154Q, chain E/F, )
31: VAR_008065 (A155T, chain E/F, )
32: VAR_046925 (A155V, chain E/F, )
33: VAR_002179 (C165Y, chain E/F, )
34: VAR_046926 (V168A, chain E/F, )
35: VAR_002180 (V168M, chain E/F, )
36: VAR_046927 (M173V, chain E/F, )
37: VAR_008066 (E176K, chain E/F, )
38: VAR_008067 (V180A, chain E/F, )
39: VAR_008068 (T191M, chain E/F, )
40: VAR_008069 (D198V, chain E, )
41: VAR_066099 (P200L, chain E, )
42: VAR_002181 (R224H, chain E/F, )
43: VAR_008070 (A226T, chain E/F, )
44: VAR_021794 (N228K, chain E/F, )
45: VAR_046928 (N228S, chain E/F, )
46: VAR_046929 (A231P, chain E/F, )
47: VAR_008071 (D234N, chain E/F, )
48: VAR_002182 (E239K, chain E/F, )
49: VAR_002183 (T257M, chain E/F, )
50: VAR_008072 (T262M, chain E/F, )
51: VAR_021795 (T262R, chain E/F, )
52: VAR_008073 (R266G, chain E/F, )
53: VAR_008074 (R266K, chain E/F, )
54: VAR_021796 (C275Y, chain E/F, )
55: VAR_066100 (I278S, chain E/F, )
56: VAR_002184 (I278T, chain E/F, )
57: VAR_066101 (D281N, chain E/F, )
58: VAR_046932 (A288P, chain E/F, )
59: VAR_046933 (A288T, chain E/F, )
60: VAR_002185 (P290L, chain E/F, )
61: VAR_008076 (E302K, chain E/F, )
62: VAR_008077 (G305R, chain E/F, )
63: VAR_002186 (G307S, chain E/F, )
64: VAR_008078 (V320A, chain E/F, )
65: VAR_066102 (D321V, chain E/F, )
66: VAR_008079 (A331E, chain E/F, )
67: VAR_002187 (A331V, chain E/F, )
68: VAR_002188 (R336C, chain E/F, )
69: VAR_008080 (R336H, chain E/F, )
70: VAR_021797 (L338P, chain E/F, )
71: VAR_021798 (G347S, chain E/F, )
72: VAR_021799 (S349N, chain E/F, )
73: VAR_008081 (S352N, chain E/F, )
74: VAR_008082 (T353M, chain E/F, )
75: VAR_008083 (V354M, chain E/F, )
76: VAR_021800 (A355P, chain E/F, )
77: VAR_046934 (A361T, chain E/F, )
78: VAR_008084 (R369C, chain E/F, )
79: VAR_002189 (R369H, chain E/F, )
80: VAR_008085 (C370Y, chain E/F, )
81: VAR_002190 (V371M, chain E/F, )
82: VAR_046935 (D376N, chain E/F, )
83: VAR_021801 (R379Q, chain E/F, )
84: VAR_046936 (R379W, chain E/F, )
85: VAR_002191 (K384E, chain E/F, )
86: VAR_008086 (K384N, chain E/F, )
87: VAR_008087 (M391I, chain E/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_008049
P
49
L
CBS_HUMAN
Disease (CBSD)
---
E/F
P
49
L
02
UniProt
VAR_008050
R
58
W
CBS_HUMAN
Disease (CBSD)
---
E/F
R
58
W
03
UniProt
VAR_021790
H
65
R
CBS_HUMAN
Disease (CBSD)
---
E/F
H
65
R
04
UniProt
VAR_046922
A
69
P
CBS_HUMAN
Polymorphism
17849313
E/F
A
69
P
05
UniProt
VAR_002171
P
78
R
CBS_HUMAN
Disease (CBSD)
---
E/F
P
78
R
06
UniProt
VAR_008051
G
85
R
CBS_HUMAN
Disease (CBSD)
---
E/F
G
85
R
07
UniProt
VAR_002172
P
88
S
CBS_HUMAN
Disease (CBSD)
---
E/F
P
88
S
08
UniProt
VAR_021791
L
101
P
CBS_HUMAN
Disease (CBSD)
---
E/F
L
101
P
09
UniProt
VAR_002173
K
102
N
CBS_HUMAN
Disease (CBSD)
---
E/F
K
102
N
10
UniProt
VAR_008052
K
102
Q
CBS_HUMAN
Disease (CBSD)
34040148
E/F
K
102
Q
11
UniProt
VAR_021792
C
109
R
CBS_HUMAN
Disease (CBSD)
---
E/F
C
109
R
12
UniProt
VAR_002174
A
114
V
CBS_HUMAN
Disease (CBSD)
---
E/F
A
114
V
13
UniProt
VAR_008053
G
116
R
CBS_HUMAN
Disease (CBSD)
---
E/F
G
116
R
14
UniProt
VAR_008054
R
121
C
CBS_HUMAN
Disease (CBSD)
---
E/F
R
121
C
15
UniProt
VAR_008055
R
121
H
CBS_HUMAN
Disease (CBSD)
---
E/F
R
121
H
16
UniProt
VAR_008056
R
121
L
CBS_HUMAN
Disease (CBSD)
---
E/F
R
121
L
17
UniProt
VAR_046923
R
125
P
CBS_HUMAN
Disease (CBSD)
---
E/F
R
125
P
18
UniProt
VAR_002175
R
125
Q
CBS_HUMAN
Disease (CBSD)
---
E/F
R
125
Q
19
UniProt
VAR_008057
R
125
W
CBS_HUMAN
Disease (CBSD)
---
E/F
R
125
W
20
UniProt
VAR_008058
M
126
V
CBS_HUMAN
Disease (CBSD)
---
E/F
M
126
V
21
UniProt
VAR_008059
E
128
D
CBS_HUMAN
Disease (CBSD)
---
E/F
E
128
D
22
UniProt
VAR_002176
E
131
D
CBS_HUMAN
Disease (CBSD)
---
E/F
E
131
D
23
UniProt
VAR_008060
G
139
R
CBS_HUMAN
Disease (CBSD)
---
E/F
G
139
R
24
UniProt
VAR_021793
I
143
M
CBS_HUMAN
Disease (CBSD)
---
E/F
I
143
M
25
UniProt
VAR_002177
E
144
K
CBS_HUMAN
Disease (CBSD)
---
E/F
E
144
K
26
UniProt
VAR_002178
P
145
L
CBS_HUMAN
Disease (CBSD)
---
E/F
P
145
L
27
UniProt
VAR_008061
G
148
R
CBS_HUMAN
Disease (CBSD)
---
E/F
G
148
R
28
UniProt
VAR_008062
G
151
R
CBS_HUMAN
Disease (CBSD)
---
E/F
G
151
R
29
UniProt
VAR_008064
I
152
M
CBS_HUMAN
Disease (CBSD)
---
E/F
I
152
M
30
UniProt
VAR_046924
L
154
Q
CBS_HUMAN
Disease (CBSD)
---
E/F
L
154
Q
31
UniProt
VAR_008065
A
155
T
CBS_HUMAN
Disease (CBSD)
---
E/F
A
155
T
32
UniProt
VAR_046925
A
155
V
CBS_HUMAN
Disease (CBSD)
---
E/F
A
155
V
33
UniProt
VAR_002179
C
165
Y
CBS_HUMAN
Disease (CBSD)
---
E/F
C
165
Y
34
UniProt
VAR_046926
V
168
A
CBS_HUMAN
Disease (CBSD)
---
E/F
V
168
A
35
UniProt
VAR_002180
V
168
M
CBS_HUMAN
Disease (CBSD)
---
E/F
V
168
M
36
UniProt
VAR_046927
M
173
V
CBS_HUMAN
Disease (CBSD)
---
E/F
M
173
V
37
UniProt
VAR_008066
E
176
K
CBS_HUMAN
Disease (CBSD)
---
E/F
E
176
K
38
UniProt
VAR_008067
V
180
A
CBS_HUMAN
Disease (CBSD)
---
E/F
V
180
A
39
UniProt
VAR_008068
T
191
M
CBS_HUMAN
Disease (CBSD)
---
E/F
T
191
M
40
UniProt
VAR_008069
D
198
V
CBS_HUMAN
Disease (CBSD)
---
E
D
198
V
41
UniProt
VAR_066099
P
200
L
CBS_HUMAN
Disease (CBSD)
---
E
P
200
L
42
UniProt
VAR_002181
R
224
H
CBS_HUMAN
Disease (CBSD)
---
E/F
R
224
H
43
UniProt
VAR_008070
A
226
T
CBS_HUMAN
Disease (CBSD)
---
E/F
A
226
T
44
UniProt
VAR_021794
N
228
K
CBS_HUMAN
Disease (CBSD)
---
E/F
N
228
K
45
UniProt
VAR_046928
N
228
S
CBS_HUMAN
Disease (CBSD)
---
E/F
N
228
S
46
UniProt
VAR_046929
A
231
P
CBS_HUMAN
Disease (CBSD)
---
E/F
A
231
P
47
UniProt
VAR_008071
D
234
N
CBS_HUMAN
Disease (CBSD)
---
E/F
D
234
N
48
UniProt
VAR_002182
E
239
K
CBS_HUMAN
Disease (CBSD)
---
E/F
E
239
K
49
UniProt
VAR_002183
T
257
M
CBS_HUMAN
Disease (CBSD)
---
E/F
T
257
M
50
UniProt
VAR_008072
T
262
M
CBS_HUMAN
Disease (CBSD)
---
E/F
T
262
M
51
UniProt
VAR_021795
T
262
R
CBS_HUMAN
Disease (CBSD)
---
E/F
T
262
R
52
UniProt
VAR_008073
R
266
G
CBS_HUMAN
Disease (CBSD)
---
E/F
R
266
G
53
UniProt
VAR_008074
R
266
K
CBS_HUMAN
Disease (CBSD)
28934275
E/F
R
266
K
54
UniProt
VAR_021796
C
275
Y
CBS_HUMAN
Disease (CBSD)
---
E/F
C
275
Y
55
UniProt
VAR_066100
I
278
S
CBS_HUMAN
Disease (CBSD)
---
E/F
I
278
S
56
UniProt
VAR_002184
I
278
T
CBS_HUMAN
Disease (CBSD)
5742905
E/F
I
278
T
57
UniProt
VAR_066101
D
281
N
CBS_HUMAN
Disease (CBSD)
---
E/F
D
281
N
58
UniProt
VAR_046932
A
288
P
CBS_HUMAN
Disease (CBSD)
---
E/F
A
288
P
59
UniProt
VAR_046933
A
288
T
CBS_HUMAN
Disease (CBSD)
---
E/F
A
288
T
60
UniProt
VAR_002185
P
290
L
CBS_HUMAN
Disease (CBSD)
---
E/F
P
290
L
61
UniProt
VAR_008076
E
302
K
CBS_HUMAN
Disease (CBSD)
---
E/F
E
302
K
62
UniProt
VAR_008077
G
305
R
CBS_HUMAN
Disease (CBSD)
---
E/F
G
305
R
63
UniProt
VAR_002186
G
307
S
CBS_HUMAN
Disease (CBSD)
---
E/F
G
307
S
64
UniProt
VAR_008078
V
320
A
CBS_HUMAN
Disease (CBSD)
---
E/F
V
320
A
65
UniProt
VAR_066102
D
321
V
CBS_HUMAN
Disease (CBSD)
---
E/F
D
321
V
66
UniProt
VAR_008079
A
331
E
CBS_HUMAN
Disease (CBSD)
---
E/F
A
331
E
67
UniProt
VAR_002187
A
331
V
CBS_HUMAN
Disease (CBSD)
---
E/F
A
331
V
68
UniProt
VAR_002188
R
336
C
CBS_HUMAN
Disease (CBSD)
---
E/F
R
336
C
69
UniProt
VAR_008080
R
336
H
CBS_HUMAN
Disease (CBSD)
---
E/F
R
336
H
70
UniProt
VAR_021797
L
338
P
CBS_HUMAN
Disease (CBSD)
---
E/F
L
338
P
71
UniProt
VAR_021798
G
347
S
CBS_HUMAN
Disease (CBSD)
---
E/F
G
347
S
72
UniProt
VAR_021799
S
349
N
CBS_HUMAN
Disease (CBSD)
---
E/F
S
349
N
73
UniProt
VAR_008081
S
352
N
CBS_HUMAN
Disease (CBSD)
---
E/F
S
352
N
74
UniProt
VAR_008082
T
353
M
CBS_HUMAN
Disease (CBSD)
---
E/F
T
353
M
75
UniProt
VAR_008083
V
354
M
CBS_HUMAN
Disease (CBSD)
---
E/F
V
354
M
76
UniProt
VAR_021800
A
355
P
CBS_HUMAN
Disease (CBSD)
---
E/F
A
355
P
77
UniProt
VAR_046934
A
361
T
CBS_HUMAN
Disease (CBSD)
---
E/F
A
361
T
78
UniProt
VAR_008084
R
369
C
CBS_HUMAN
Disease (CBSD)
117687681
E/F
R
369
C
79
UniProt
VAR_002189
R
369
H
CBS_HUMAN
Disease (CBSD)
11700812
E/F
R
369
H
80
UniProt
VAR_008085
C
370
Y
CBS_HUMAN
Disease (CBSD)
---
E/F
C
370
Y
81
UniProt
VAR_002190
V
371
M
CBS_HUMAN
Disease (CBSD)
---
E/F
V
371
M
82
UniProt
VAR_046935
D
376
N
CBS_HUMAN
Disease (CBSD)
---
E/F
D
376
N
83
UniProt
VAR_021801
R
379
Q
CBS_HUMAN
Disease (CBSD)
---
E/F
R
379
Q
84
UniProt
VAR_046936
R
379
W
CBS_HUMAN
Disease (CBSD)
---
E/F
R
379
W
85
UniProt
VAR_002191
K
384
E
CBS_HUMAN
Disease (CBSD)
---
E/F
K
384
E
86
UniProt
VAR_008086
K
384
N
CBS_HUMAN
Disease (CBSD)
---
E/F
K
384
N
87
UniProt
VAR_008087
M
391
I
CBS_HUMAN
Disease (CBSD)
---
E/F
M
391
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: CYS_SYNTHASE (E:108-126,F:108-126)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYS_SYNTHASE
PS00901
Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site.
CBS_HUMAN
108-126
2
-
-
-
-
E:108-126
F:108-126
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1m54a_ (A:)
1b: SCOP_d1m54e_ (E:)
1c: SCOP_d1m54f_ (F:)
1d: SCOP_d1m54b_ (B:)
1e: SCOP_d1m54c_ (C:)
1f: SCOP_d1m54d_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Tryptophan synthase beta subunit-like PLP-dependent enzymes
(165)
Superfamily
:
Tryptophan synthase beta subunit-like PLP-dependent enzymes
(165)
Family
:
Tryptophan synthase beta subunit-like PLP-dependent enzymes
(120)
Protein domain
:
Cystathionine beta-synthase
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1m54a_
A:
1b
d1m54e_
E:
1c
d1m54f_
F:
1d
d1m54b_
B:
1e
d1m54c_
C:
1f
d1m54d_
D:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1m54A01 (A:74-112,A:236-390)
1b: CATH_1m54E01 (E:74-112,E:236-390)
1c: CATH_1m54F01 (F:74-112,F:236-390)
1d: CATH_1m54E02 (E:113-222)
1e: CATH_1m54A02 (A:113-222)
1f: CATH_1m54C02 (C:113-222)
1g: CATH_1m54D02 (D:113-222)
1h: CATH_1m54B02 (B:113-222)
1i: CATH_1m54F02 (F:113-222)
1j: CATH_1m54B01 (B:74-112,B:236-390)
1k: CATH_1m54C01 (C:74-112,C:236-390)
1l: CATH_1m54D01 (D:74-112,D:236-390)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1100, no name defined]
(77)
Human (Homo sapiens)
(4)
1a
1m54A01
A:74-112,A:236-390
1b
1m54E01
E:74-112,E:236-390
1c
1m54F01
F:74-112,F:236-390
1d
1m54E02
E:113-222
1e
1m54A02
A:113-222
1f
1m54C02
C:113-222
1g
1m54D02
D:113-222
1h
1m54B02
B:113-222
1i
1m54F02
F:113-222
1j
1m54B01
B:74-112,B:236-390
1k
1m54C01
C:74-112,C:236-390
1l
1m54D01
D:74-112,D:236-390
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_PALP_1m54F01 (F:80-376)
1b: PFAM_PALP_1m54F02 (F:80-376)
1c: PFAM_PALP_1m54F03 (F:80-376)
1d: PFAM_PALP_1m54F04 (F:80-376)
1e: PFAM_PALP_1m54F05 (F:80-376)
1f: PFAM_PALP_1m54F06 (F:80-376)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: PALP]
(67)
Family
:
PALP
(67)
Homo sapiens (Human)
(6)
1a
PALP-1m54F01
F:80-376
1b
PALP-1m54F02
F:80-376
1c
PALP-1m54F03
F:80-376
1d
PALP-1m54F04
F:80-376
1e
PALP-1m54F05
F:80-376
1f
PALP-1m54F06
F:80-376
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain E
Chain F
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (340 KB)
Header - Asym.Unit
Biol.Unit 1 (114 KB)
Header - Biol.Unit 1
Biol.Unit 2 (113 KB)
Header - Biol.Unit 2
Biol.Unit 3 (114 KB)
Header - Biol.Unit 3
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1M54
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help