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3IN8
Asym. Unit
Info
Asym.Unit (26 KB)
Biol.Unit 1 (41 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE GRB2 SH2 DOMAIN IN COMPLEX WITH A FLEXIBLE AC-PTYR-ILE-ASN-NH2 TRIPEPTIDE MIMIC
Authors
:
A. P. Benfield, J. H. Clements
Date
:
11 Aug 09 (Deposition) - 17 Nov 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Ligand Preorganization, Golgi Apparatus, Peptide Mimics, Host-Virus Interaction, Phosphoprotein, Sh2 Domain, Sh3, Signaling Protein, Signaling Protein-Pseudopeptide Ligand Complex, Signaling Protein- Peptide Complex, Signaling Protein-Peptide Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. E. Delorbe, J. H. Clements, M. G. Teresk, A. P. Benfield, H. R. Plake, L. E. Millspaugh, S. F. Martin
Thermodynamic And Structural Effects Of Conformational Constraints In Protein-Ligand Interactions. Entropic Paradoxy Associated With Ligand Preorganization.
J. Am. Chem. Soc. V. 131 16758 2009
(for further references see the
PDB file header
)
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: FORMIC ACID (FMTa)
2a: N-{(2S)-4-(METHYLAMINO)-4-OXO-2-[4... (FYIa)
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Label:
No.
Name
Count
Type
Full Name
1
FMT
1
Ligand/Ion
FORMIC ACID
2
FYI
1
Ligand/Ion
N-{(2S)-4-(METHYLAMINO)-4-OXO-2-[4-(PHOSPHONOOXY)BENZYL]BUTANOYL}-L-ISOLEUCYL-L-ASPARTAMIDE
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:12 , HOH A:37 , HOH A:38 , ARG A:67 , ARG A:78 , ARG A:86 , SER A:88 , SER A:90 , SER A:96 , HIS A:107 , PHE A:108 , LYS A:109 , LEU A:120 , TRP A:121 , GLU A:152 , VAL A:154 , PRO A:155 , HOH A:189 , HOH A:207 , HOH A:230
BINDING SITE FOR RESIDUE FYI A 1
2
AC2
SOFTWARE
HOH A:4 , HOH A:35 , GLN A:77 , ARG A:78 , HIS A:79 , LYS A:109 , GLU A:152
BINDING SITE FOR RESIDUE FMT A 170
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: SH2 (A:60-152)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SH2
PS50001
Src homology 2 (SH2) domain profile.
GRB2_HUMAN
60-152
1
A:60-152
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Exons
(3, 3)
Info
All Exons
Exon 1.4 (A:55-59)
Exon 1.6 (A:59-100)
Exon 1.7 (A:100-155)
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All Exon Boundaries
1: Boundary 1.3a/1.4
2: Boundary 1.4/1.6
3: Boundary 1.6/1.7
4: Boundary 1.7/1.8b
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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
1.3a
ENST00000392564
3a
ENSE00001512384
chr17:
73389945-73389632
314
GRB2_HUMAN
1-26
26
0
-
-
1.4
ENST00000392564
4
ENSE00000387085
chr17:
73328878-73328781
98
GRB2_HUMAN
27-59
33
1
A:55-59
5
1.6
ENST00000392564
6
ENSE00000855724
chr17:
73322101-73321979
123
GRB2_HUMAN
59-100
42
1
A:59-100
42
1.7
ENST00000392564
7
ENSE00000744359
chr17:
73317908-73317740
169
GRB2_HUMAN
100-156
57
1
A:100-155
56
1.8b
ENST00000392564
8b
ENSE00001512383
chr17:
73316634-73314157
2478
GRB2_HUMAN
157-217
61
0
-
-
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3in8a_ (A:)
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)
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)
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)
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)
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)
(
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
SH2-like
(260)
Superfamily
:
SH2 domain
(260)
Family
:
SH2 domain
(225)
Protein domain
:
Growth factor receptor-bound protein 2 (GRB2)
(34)
Human (Homo sapiens) [TaxId: 9606]
(34)
1a
d3in8a_
A:
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_3in8A00 (A:55-155)
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Organisms
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)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
SHC Adaptor Protein
(206)
Homologous Superfamily
:
SHC Adaptor Protein
(206)
Human (Homo sapiens)
(147)
1a
3in8A00
A:55-155
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Pfam Domains
(0, 0)
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all PFAM domains
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Chain A
Asymmetric Unit 1
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