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1TU4
Asym. Unit
Info
Asym.Unit (124 KB)
Biol.Unit 1 (34 KB)
Biol.Unit 10 (61 KB)
Biol.Unit 2 (31 KB)
Biol.Unit 3 (32 KB)
Biol.Unit 4 (31 KB)
Biol.Unit 5 (228 KB)
Biol.Unit 6 (116 KB)
Biol.Unit 7 (118 KB)
Biol.Unit 8 (115 KB)
Biol.Unit 9 (59 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RAB5-GDP COMPLEX
Authors
:
G. Zhu, P. Zhai, J. Liu, S. Terzyan, G. Li, X. C. Zhang
Date
:
24 Jun 04 (Deposition) - 05 Oct 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
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)
Biol. Unit 5: A,B,C,D (2x)
Biol. Unit 6: A,B,C,D (1x)
Biol. Unit 7: A,B (2x)
Biol. Unit 8: C,D (2x)
Biol. Unit 9: C,D (1x)
Biol. Unit 10: A,B (1x)
Keywords
:
Rab5, Gtpase, Protein Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Zhu, P. Zhai, J. Liu, S. Terzyan, G. Li, X. C. Zhang
Structural Basis Of Rab5-Rabaptin5 Interaction In Endocytosis
Nat. Struct. Mol. Biol. V. 11 975 2004
(for further references see the
PDB file header
)
[
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]
Hetero Components
(4, 32)
Info
All Hetero Components
1a: COBALT (II) ION (COa)
1b: COBALT (II) ION (COb)
1c: COBALT (II) ION (COc)
1d: COBALT (II) ION (COd)
1e: COBALT (II) ION (COe)
1f: COBALT (II) ION (COf)
2a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
2b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
2c: GUANOSINE-5'-DIPHOSPHATE (GDPc)
2d: GUANOSINE-5'-DIPHOSPHATE (GDPd)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CO
6
Ligand/Ion
COBALT (II) ION
2
GDP
4
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
3
MSE
16
Mod. Amino Acid
SELENOMETHIONINE
4
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(16, 16)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:34 , HOH A:301 , HOH A:302 , HOH A:308 , GDP A:1200 , HOH D:303
BINDING SITE FOR RESIDUE CO A 1201
02
AC2
SOFTWARE
SER B:34 , HOH B:304 , HOH B:305 , HOH B:306 , HOH B:307 , GDP B:2200
BINDING SITE FOR RESIDUE CO B 2201
03
AC3
SOFTWARE
SER C:34 , HOH C:309 , HOH C:310 , HOH C:311 , HOH C:312 , GDP C:3200
BINDING SITE FOR RESIDUE CO C 3201
04
AC4
SOFTWARE
SER D:34 , HOH D:313 , HOH D:314 , HOH D:315 , HOH D:316 , GDP D:4200
BINDING SITE FOR RESIDUE CO D 4201
05
AC5
SOFTWARE
HIS A:83 , HOH A:395 , GLU B:80 , HIS B:83 , HOH B:396
BINDING SITE FOR RESIDUE CO B 251
06
AC6
SOFTWARE
HIS C:83 , HOH C:397 , HOH C:398 , GLU D:80 , HIS D:83
BINDING SITE FOR RESIDUE CO D 252
07
AC7
SOFTWARE
GLN B:79 , GLU B:80 , ARG B:81 , HOH B:353
BINDING SITE FOR RESIDUE SO4 B 261
08
AC8
SOFTWARE
ALA D:77 , GLY D:78 , GLN D:79 , HOH D:315 , HOH D:316
BINDING SITE FOR RESIDUE SO4 D 262
09
AC9
SOFTWARE
GLN D:79 , GLU D:80 , ARG D:81 , HOH D:490
BINDING SITE FOR RESIDUE SO4 D 263
10
BC1
SOFTWARE
ALA B:77 , GLY B:78 , GLN B:79 , HOH B:306 , HOH B:307 , HOH B:608
BINDING SITE FOR RESIDUE SO4 B 264
11
BC2
SOFTWARE
ARG A:81 , HOH A:552 , GLN B:121 , ASN D:16
BINDING SITE FOR RESIDUE SO4 D 265
12
BC3
SOFTWARE
GLN D:121 , HOH D:522 , HOH D:563
BINDING SITE FOR RESIDUE SO4 D 266
13
BC4
SOFTWARE
GLU A:28 , ALA A:30 , VAL A:31 , GLY A:32 , LYS A:33 , SER A:34 , SER A:35 , ASN A:133 , LYS A:134 , ASP A:136 , LEU A:137 , SER A:163 , ALA A:164 , LYS A:165 , HOH A:302 , HOH A:308 , HOH A:414 , HOH A:433 , HOH A:461 , CO A:1201
BINDING SITE FOR RESIDUE GDP A 1200
14
BC5
SOFTWARE
GLN A:119 , ARG A:120 , ALA A:122 , SER A:123 , PRO A:124 , ALA B:30 , VAL B:31 , GLY B:32 , LYS B:33 , SER B:34 , SER B:35 , ASN B:133 , LYS B:134 , ASP B:136 , LEU B:137 , SER B:163 , ALA B:164 , LYS B:165 , HOH B:307 , HOH B:317 , HOH B:339 , HOH B:345 , HOH B:435 , HOH B:521 , HOH B:595 , CO B:2201
BINDING SITE FOR RESIDUE GDP B 2200
15
BC6
SOFTWARE
GLU C:28 , ALA C:30 , VAL C:31 , GLY C:32 , LYS C:33 , SER C:34 , SER C:35 , ASN C:133 , LYS C:134 , ASP C:136 , SER C:163 , ALA C:164 , LYS C:165 , HOH C:310 , HOH C:311 , HOH C:422 , HOH C:523 , CO C:3201
BINDING SITE FOR RESIDUE GDP C 3200
16
BC7
SOFTWARE
GLN C:119 , ARG C:120 , ALA C:122 , SER C:123 , PRO C:124 , ALA D:30 , VAL D:31 , GLY D:32 , LYS D:33 , SER D:34 , SER D:35 , ASN D:133 , LYS D:134 , ASP D:136 , LEU D:137 , SER D:163 , ALA D:164 , HOH D:313 , HOH D:316 , CO D:4201
BINDING SITE FOR RESIDUE GDP D 4200
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: RAB (A:15-183,C:15-183)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RAB
PS51419
small GTPase Rab1 family profile.
RAB5A_HUMAN
15-215
2
A:15-183
C:15-183
[
close PROSITE info
]
Exons
(5, 20)
Info
All Exons
Exon 1.2b (A:15-55 | B:18-55 (gaps) | C:15-55...)
Exon 1.4c (A:55-105 | B:55-105 | C:55-105 | D...)
Exon 1.5b (A:106-146 | B:106-146 | C:106-146 ...)
Exon 1.6a (A:147-178 | B:147-178 | C:147-178 ...)
Exon 1.7e (A:178-183 | B:178-182 | C:178-183 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1a/1.2b
2: Boundary 1.2b/1.4c
3: Boundary 1.4c/1.5b
4: Boundary 1.5b/1.6a
5: Boundary 1.6a/1.7e
6: Boundary 1.7e/-
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
1.1a
ENST00000273047
1a
ENSE00001769725
chr3:
19988571-19989013
443
RAB5A_HUMAN
-
0
0
-
-
1.2b
ENST00000273047
2b
ENSE00001162720
chr3:
19992298-19992553
256
RAB5A_HUMAN
1-55
55
4
A:15-55
B:18-55 (gaps)
C:15-55
D:16-55 (gaps)
41
38
41
40
1.4c
ENST00000273047
4c
ENSE00001691424
chr3:
20017093-20017244
152
RAB5A_HUMAN
55-105
51
4
A:55-105
B:55-105
C:55-105
D:55-105
51
51
51
51
1.5b
ENST00000273047
5b
ENSE00001783762
chr3:
20017539-20017661
123
RAB5A_HUMAN
106-146
41
4
A:106-146
B:106-146
C:106-146
D:106-146
41
41
41
41
1.6a
ENST00000273047
6a
ENSE00001688303
chr3:
20019802-20019895
94
RAB5A_HUMAN
147-178
32
4
A:147-178
B:147-178
C:147-178
D:147-178
32
32
32
32
1.7e
ENST00000273047
7e
ENSE00001368096
chr3:
20025200-20026667
1468
RAB5A_HUMAN
178-215
38
4
A:178-183
B:178-182
C:178-183
D:178-182
6
5
6
5
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1tu4a_ (A:)
1b: SCOP_d1tu4b_ (B:)
1c: SCOP_d1tu4c_ (C:)
1d: SCOP_d1tu4d_ (D:)
View:
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Classes
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)
(
)
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
G proteins
(693)
Protein domain
:
Rab5a
(12)
Human (Homo sapiens) [TaxId: 9606]
(12)
1a
d1tu4a_
A:
1b
d1tu4b_
B:
1c
d1tu4c_
C:
1d
d1tu4d_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1tu4A00 (A:15-183)
1b: CATH_1tu4C00 (C:15-183)
1c: CATH_1tu4D00 (D:16-182)
1d: CATH_1tu4B00 (B:18-182)
View:
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Classes
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(
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(
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Human (Homo sapiens)
(413)
1a
1tu4A00
A:15-183
1b
1tu4C00
C:15-183
1c
1tu4D00
D:16-182
1d
1tu4B00
B:18-182
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Ras_1tu4D01 (D:22-182)
1b: PFAM_Ras_1tu4D02 (D:22-182)
1c: PFAM_Ras_1tu4D03 (D:22-182)
1d: PFAM_Ras_1tu4D04 (D:22-182)
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Clans
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(
)
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(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
Ras
(176)
Homo sapiens (Human)
(141)
1a
Ras-1tu4D01
D:22-182
1b
Ras-1tu4D02
D:22-182
1c
Ras-1tu4D03
D:22-182
1d
Ras-1tu4D04
D:22-182
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Asym.Unit (124 KB)
Header - Asym.Unit
Biol.Unit 1 (34 KB)
Header - Biol.Unit 1
Biol.Unit 10 (61 KB)
Header - Biol.Unit 10
Biol.Unit 2 (31 KB)
Header - Biol.Unit 2
Biol.Unit 3 (32 KB)
Header - Biol.Unit 3
Biol.Unit 4 (31 KB)
Header - Biol.Unit 4
Biol.Unit 5 (228 KB)
Header - Biol.Unit 5
Biol.Unit 6 (116 KB)
Header - Biol.Unit 6
Biol.Unit 7 (118 KB)
Header - Biol.Unit 7
Biol.Unit 8 (115 KB)
Header - Biol.Unit 8
Biol.Unit 9 (59 KB)
Header - Biol.Unit 9
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