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1T77
Asym. Unit
Info
Asym.Unit (285 KB)
Biol.Unit 1 (73 KB)
Biol.Unit 2 (74 KB)
Biol.Unit 3 (74 KB)
Biol.Unit 4 (73 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE PH-BEACH DOMAINS OF HUMAN LRBA/BGL
Authors
:
D. Gebauer, J. Li, G. Jogl, Y. Shen, D. G. Myszka, L. Tong
Date
:
08 May 04 (Deposition) - 21 Dec 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Ph-Beach Domains; Vesicle Trafficking; Signal Transduction, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Gebauer, J. Li, G. Jogl, Y. Shen, D. G. Myszka, L. Tong
Crystal Structure Of The Ph-Beach Domains Of Human Lrba/Bgl
Biochemistry V. 43 14873 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_035884 (G2274R, chain A/B/C/D, )
2: VAR_LRBA_HUMAN_CCDS3773_1_02 (G2274R, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_035884
G
2274
R
LRBA_HUMAN
Unclassified
---
A/B/C/D
G
2274
R
2
CancerSNP
VAR_LRBA_HUMAN_CCDS3773_1_02
*
G
2274
R
LRBA_HUMAN
Disease (Breast cancer)
---
A/B/C/D
G
2274
R
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: BEACH (A:2200-2489,B:2200-2489,C:2200-248...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BEACH
PS50197
BEACH domain profile.
LRBA_HUMAN
2200-2489
4
A:2200-2489
B:2200-2489
C:2200-2489
D:2200-2489
[
close PROSITE info
]
Exons
(11, 44)
Info
All Exons
Exon 1.44 (A:2076-2076 | B:2076-2076 | C:2076...)
Exon 1.45 (A:2076-2121 | B:2076-2121 | C:2076...)
Exon 1.47b (A:2122-2161 | B:2122-2161 | C:2122...)
Exon 1.48 (A:2161-2195 | B:2161-2195 | C:2161...)
Exon 1.49 (A:2195-2234 | B:2195-2234 | C:2195...)
Exon 1.50 (A:2234-2271 | B:2234-2271 | C:2234...)
Exon 1.51 (A:2272-2318 | B:2272-2318 | C:2272...)
Exon 1.52 (A:2319-2358 | B:2319-2358 | C:2319...)
Exon 1.53 (A:2359-2409 | B:2359-2409 | C:2359...)
Exon 1.54 (A:2410-2465 | B:2410-2465 | C:2410...)
Exon 1.55 (A:2466-2489 | B:2466-2489 | C:2466...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.43/1.44
02: Boundary 1.44/1.45
03: Boundary 1.45/1.47b
04: Boundary 1.47b/1.48
05: Boundary 1.48/1.49
06: Boundary 1.49/1.50
07: Boundary 1.50/1.51
08: Boundary 1.51/1.52
09: Boundary 1.52/1.53
10: Boundary 1.53/1.54
11: Boundary 1.54/1.55
12: Boundary 1.55/1.56b
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1b
ENST00000357115
1b
ENSE00002062602
chr4:
151936649-151936625
25
LRBA_HUMAN
-
0
0
-
-
1.3a
ENST00000357115
3a
ENSE00001428255
chr4:
151936013-151935579
435
LRBA_HUMAN
1-72
72
0
-
-
1.4
ENST00000357115
4
ENSE00001250476
chr4:
151850217-151849986
232
LRBA_HUMAN
73-150
78
0
-
-
1.5
ENST00000357115
5
ENSE00000740094
chr4:
151849768-151849668
101
LRBA_HUMAN
150-183
34
0
-
-
1.6
ENST00000357115
6
ENSE00000740095
chr4:
151842445-151842350
96
LRBA_HUMAN
184-215
32
0
-
-
1.7
ENST00000357115
7
ENSE00001777660
chr4:
151837890-151837769
122
LRBA_HUMAN
216-256
41
0
-
-
1.8
ENST00000357115
8
ENSE00000821062
chr4:
151837679-151837553
127
LRBA_HUMAN
256-298
43
0
-
-
1.9
ENST00000357115
9
ENSE00000740096
chr4:
151836879-151836760
120
LRBA_HUMAN
299-338
40
0
-
-
1.10
ENST00000357115
10
ENSE00000740097
chr4:
151835493-151835347
147
LRBA_HUMAN
339-387
49
0
-
-
1.11
ENST00000357115
11
ENSE00000740098
chr4:
151830009-151829812
198
LRBA_HUMAN
388-453
66
0
-
-
1.12
ENST00000357115
12
ENSE00000740099
chr4:
151829619-151829486
134
LRBA_HUMAN
454-498
45
0
-
-
1.13
ENST00000357115
13
ENSE00000740100
chr4:
151827557-151827449
109
LRBA_HUMAN
498-534
37
0
-
-
1.14
ENST00000357115
14
ENSE00000821061
chr4:
151827142-151826990
153
LRBA_HUMAN
535-585
51
0
-
-
1.15
ENST00000357115
15
ENSE00000740101
chr4:
151821369-151821201
169
LRBA_HUMAN
586-642
57
0
-
-
1.16
ENST00000357115
16
ENSE00000821060
chr4:
151818970-151818891
80
LRBA_HUMAN
642-668
27
0
-
-
1.17
ENST00000357115
17
ENSE00001250470
chr4:
151817608-151817546
63
LRBA_HUMAN
669-689
21
0
-
-
1.18
ENST00000357115
18
ENSE00000821058
chr4:
151814301-151814204
98
LRBA_HUMAN
690-722
33
0
-
-
1.19
ENST00000357115
19
ENSE00000821057
chr4:
151793907-151793815
93
LRBA_HUMAN
722-753
32
0
-
-
1.20
ENST00000357115
20
ENSE00000821054
chr4:
151792605-151792497
109
LRBA_HUMAN
753-789
37
0
-
-
1.21
ENST00000357115
21
ENSE00000821053
chr4:
151791758-151791677
82
LRBA_HUMAN
790-817
28
0
-
-
1.22
ENST00000357115
22
ENSE00000740104
chr4:
151789457-151789334
124
LRBA_HUMAN
817-858
42
0
-
-
1.23
ENST00000357115
23
ENSE00000740106
chr4:
151789015-151788823
193
LRBA_HUMAN
858-922
65
0
-
-
1.24
ENST00000357115
24
ENSE00001200926
chr4:
151774095-151773037
1059
LRBA_HUMAN
923-1275
353
0
-
-
1.25
ENST00000357115
25
ENSE00000740109
chr4:
151772054-151771876
179
LRBA_HUMAN
1276-1335
60
0
-
-
1.26a
ENST00000357115
26a
ENSE00001081827
chr4:
151770727-151770574
154
LRBA_HUMAN
1335-1386
52
0
-
-
1.27a
ENST00000357115
27a
ENSE00001081825
chr4:
151770150-151769970
181
LRBA_HUMAN
1387-1447
61
0
-
-
1.28
ENST00000357115
28
ENSE00001081822
chr4:
151765931-151765810
122
LRBA_HUMAN
1447-1487
41
0
-
-
1.29
ENST00000357115
29
ENSE00001081828
chr4:
151765359-151765252
108
LRBA_HUMAN
1488-1523
36
0
-
-
1.31
ENST00000357115
31
ENSE00001081824
chr4:
151753128-151752969
160
LRBA_HUMAN
1524-1577
54
0
-
-
1.32
ENST00000357115
32
ENSE00001081820
chr4:
151749773-151749332
442
LRBA_HUMAN
1577-1724
148
0
-
-
1.33
ENST00000357115
33
ENSE00001081829
chr4:
151738409-151738276
134
LRBA_HUMAN
1724-1769
46
0
-
-
1.34
ENST00000357115
34
ENSE00001081823
chr4:
151729550-151729472
79
LRBA_HUMAN
1769-1795
27
0
-
-
1.35
ENST00000357115
35
ENSE00001081826
chr4:
151727556-151727423
134
LRBA_HUMAN
1795-1840
46
0
-
-
1.36
ENST00000357115
36
ENSE00001081818
chr4:
151719294-151719233
62
LRBA_HUMAN
1840-1860
21
0
-
-
1.37
ENST00000357115
37
ENSE00001619686
chr4:
151682999-151682935
65
LRBA_HUMAN
1861-1882
22
0
-
-
1.38
ENST00000357115
38
ENSE00001081830
chr4:
151656518-151656410
109
LRBA_HUMAN
1882-1918
37
0
-
-
1.40b
ENST00000357115
40b
ENSE00001250081
chr4:
151604869-151604703
167
LRBA_HUMAN
1919-1974
56
0
-
-
1.42
ENST00000357115
42
ENSE00001250073
chr4:
151520283-151520159
125
LRBA_HUMAN
1974-2016
43
0
-
-
1.43
ENST00000357115
43
ENSE00001249966
chr4:
151518267-151518235
33
LRBA_HUMAN
2016-2027
12
0
-
-
1.44
ENST00000357115
44
ENSE00001250067
chr4:
151512011-151511865
147
LRBA_HUMAN
2027-2076
50
4
A:2076-2076
B:2076-2076
C:2076-2076
D:2076-2076
1
1
1
1
1.45
ENST00000357115
45
ENSE00001250060
chr4:
151509336-151509200
137
LRBA_HUMAN
2076-2121
46
4
A:2076-2121
B:2076-2121
C:2076-2121
D:2076-2121
46
46
46
46
1.47b
ENST00000357115
47b
ENSE00001081814
chr4:
151412187-151412070
118
LRBA_HUMAN
2122-2161
40
4
A:2122-2161
B:2122-2161
C:2122-2161
D:2122-2161
40
40
40
40
1.48
ENST00000357115
48
ENSE00001081812
chr4:
151408986-151408884
103
LRBA_HUMAN
2161-2195
35
4
A:2161-2195
B:2161-2195
C:2161-2195
D:2161-2195
35
35
35
35
1.49
ENST00000357115
49
ENSE00001081811
chr4:
151392891-151392776
116
LRBA_HUMAN
2195-2234
40
4
A:2195-2234
B:2195-2234
C:2195-2234
D:2195-2234
40
40
40
40
1.50
ENST00000357115
50
ENSE00001081817
chr4:
151388937-151388825
113
LRBA_HUMAN
2234-2271
38
4
A:2234-2271
B:2234-2271
C:2234-2271
D:2234-2271
38
38
38
38
1.51
ENST00000357115
51
ENSE00001081806
chr4:
151358016-151357876
141
LRBA_HUMAN
2272-2318
47
4
A:2272-2318
B:2272-2318
C:2272-2318
D:2272-2318
47
47
47
47
1.52
ENST00000357115
52
ENSE00001081809
chr4:
151356860-151356741
120
LRBA_HUMAN
2319-2358
40
4
A:2319-2358
B:2319-2358
C:2319-2358
D:2319-2358
40
40
40
40
1.53
ENST00000357115
53
ENSE00001081813
chr4:
151336742-151336590
153
LRBA_HUMAN
2359-2409
51
4
A:2359-2409
B:2359-2409
C:2359-2409
D:2359-2409
51
51
51
51
1.54
ENST00000357115
54
ENSE00001782930
chr4:
151271311-151271144
168
LRBA_HUMAN
2410-2465
56
4
A:2410-2465
B:2410-2465
C:2410-2465
D:2410-2465
56
56
56
56
1.55
ENST00000357115
55
ENSE00001002329
chr4:
151247050-151246961
90
LRBA_HUMAN
2466-2495
30
4
A:2466-2489
B:2466-2489
C:2466-2489
D:2466-2489
24
24
24
24
1.56b
ENST00000357115
56b
ENSE00001081815
chr4:
151242520-151242343
178
LRBA_HUMAN
2496-2555
60
0
-
-
1.57b
ENST00000357115
57b
ENSE00001249949
chr4:
151236775-151236713
63
LRBA_HUMAN
2555-2576
22
0
-
-
1.58b
ENST00000357115
58b
ENSE00001002330
chr4:
151231536-151231381
156
LRBA_HUMAN
2576-2628
53
0
-
-
1.59b
ENST00000357115
59b
ENSE00001002331
chr4:
151223944-151223777
168
LRBA_HUMAN
2628-2684
57
0
-
-
1.60
ENST00000357115
60
ENSE00001002334
chr4:
151207186-151207085
102
LRBA_HUMAN
2684-2718
35
0
-
-
1.61
ENST00000357115
61
ENSE00001081805
chr4:
151203798-151203602
197
LRBA_HUMAN
2718-2783
66
0
-
-
1.62
ENST00000357115
62
ENSE00001081810
chr4:
151199156-151199005
152
LRBA_HUMAN
2784-2834
51
0
-
-
1.63d
ENST00000357115
63d
ENSE00002087376
chr4:
151186964-151185811
1154
LRBA_HUMAN
2834-2863
30
0
-
-
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1t77a1 (A:2186-2489)
1b: SCOP_d1t77b1 (B:2186-2489)
1c: SCOP_d1t77c1 (C:2186-2489)
1d: SCOP_d1t77d1 (D:2186-2489)
2a: SCOP_d1t77a2 (A:2076-2185)
2b: SCOP_d1t77b2 (B:2076-2185)
2c: SCOP_d1t77c2 (C:2076-2185)
2d: SCOP_d1t77d2 (D:2076-2185)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
BEACH domain
(2)
Superfamily
:
BEACH domain
(2)
Family
:
BEACH domain
(2)
Protein domain
:
Lipopolysaccharide-responsive and beige-like anchor protein LRBA
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1t77a1
A:2186-2489
1b
d1t77b1
B:2186-2489
1c
d1t77c1
C:2186-2489
1d
d1t77d1
D:2186-2489
Class
:
All beta proteins
(24004)
Fold
:
PH domain-like barrel
(258)
Superfamily
:
PH domain-like
(257)
Family
:
PreBEACH PH-like domain
(2)
Protein domain
:
Lipopolysaccharide-responsive and beige-like anchor protein LRBA
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d1t77a2
A:2076-2185
2b
d1t77b2
B:2076-2185
2c
d1t77c2
C:2076-2185
2d
d1t77d2
D:2076-2185
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1t77A02 (A:2201-2489)
1b: CATH_1t77B02 (B:2201-2489)
1c: CATH_1t77C02 (C:2201-2489)
1d: CATH_1t77D02 (D:2201-2489)
2a: CATH_1t77A01 (A:2076-2180)
2b: CATH_1t77B01 (B:2076-2180)
2c: CATH_1t77C01 (C:2076-2180)
2d: CATH_1t77D01 (D:2076-2180)
View:
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Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Neurobeachin; Chain: A, domain 1
(2)
Homologous Superfamily
:
[code=1.10.1540.10, no name defined]
(2)
Human (Homo sapiens)
(2)
1a
1t77A02
A:2201-2489
1b
1t77B02
B:2201-2489
1c
1t77C02
C:2201-2489
1d
1t77D02
D:2201-2489
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
PH-domain like
(150)
Homologous Superfamily
:
PH domain-like; domain 1
(2)
Human (Homo sapiens)
(2)
2a
1t77A01
A:2076-2180
2b
1t77B01
B:2076-2180
2c
1t77C01
C:2076-2180
2d
1t77D01
D:2076-2180
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Beach_1t77D01 (D:2212-2489)
1b: PFAM_Beach_1t77D02 (D:2212-2489)
1c: PFAM_Beach_1t77D03 (D:2212-2489)
1d: PFAM_Beach_1t77D04 (D:2212-2489)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Beach]
(2)
Family
:
Beach
(2)
Homo sapiens (Human)
(2)
1a
Beach-1t77D01
D:2212-2489
1b
Beach-1t77D02
D:2212-2489
1c
Beach-1t77D03
D:2212-2489
1d
Beach-1t77D04
D:2212-2489
[
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 A
Chain B
Chain C
Chain D
Asymmetric Unit 1
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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)
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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") .
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Asym.Unit (285 KB)
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