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3L95
Biol. Unit 1
Info
Asym.Unit (216 KB)
Biol.Unit 1 (174 KB)
Biol.Unit 2 (141 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE HUMAN NOTCH1 NEGATIVE REGULATORY REGION (NRR) BOUND TO THE FAB FRAGMENT OF AN ANTAGONIST ANTIBODY
Authors
:
S. G. Hymowitz, G. P. De Leon
Date
:
04 Jan 10 (Deposition) - 09 Mar 10 (Release) - 25 Sep 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.19
Chains
:
Asym. Unit : A,B,H,L,X,Y
Biol. Unit 1: A,B,H,X,Y (1x)
Biol. Unit 2: H,L,X,Y (1x)
Keywords
:
Nrr, Fab Fragment, Antibody, Alpha-Beta-Sandwich, Sea Domain, Lnr, Lin12 Notch Cysteine-Rich, Hd Domain, Cell Cycle, Signaling Protein, Activator, Ank Repeat, Cell Membrane, Developmental Protein, Differentiation, Egf-Like Domain, Glycoprotein, Membrane, Metal- Binding, Notch Signaling Pathway, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Wu, C. Cain-Hom, L. Choy, T. J. Hagenbeek, G. P. De Leon, Y. Chen, D. Finkle, R. Venook, X. Wu, J. Ridgway, D. Schahin-Reed, G. J. Dow, A. Shelton, S. Stawicki, R. J. Watts, J. Zhang, R. Choy, P. Howard, L. Kadyk, M. Yan, J. Zha, C. A. Callahan, S. G. Hymowitz, C. W. Siebel
Therapeutic Antibody Targeting Of Individual Notch Receptors.
Nature V. 464 1052 2010
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Hetero Components
(2, 3)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
SO4
1
Ligand/Ion
SULFATE ION
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PHE B:27 , THR B:28 , TYR B:32 , GLY X:1447 , SER X:1448 , VAL X:1727
BINDING SITE FOR RESIDUE SO4 B 222
2
AC2
SOFTWARE
ASP X:1458 , ASN X:1461 , VAL X:1463 , ASP X:1476 , ASP X:1479
BINDING SITE FOR RESIDUE CA X 2001
3
AC3
SOFTWARE
TYR X:1500 , ASP X:1503 , HIS X:1505 , ASP X:1507 , ASP X:1518 , ASP X:1521
BINDING SITE FOR RESIDUE CA X 2002
4
AC4
SOFTWARE
HIS X:1540 , ASP X:1543 , HIS X:1545 , ASP X:1547 , ASP X:1558 , ASP X:1561
BINDING SITE FOR RESIDUE CA X 2003
5
AC5
SOFTWARE
HOH X:79 , LYS X:1489 , ASN X:1490 , SER X:1696 , THR X:1698 , ASP X:1699 , NAG X:2005
BINDING SITE FOR RESIDUE NAG X 2004
6
AC6
SOFTWARE
NAG X:2004
BINDING SITE FOR RESIDUE NAG X 2005
7
AC7
SOFTWARE
ASN Y:1461 , VAL Y:1463 , SER Y:1465 , ASP Y:1476
BINDING SITE FOR RESIDUE CA Y 2001
8
AC8
SOFTWARE
TYR Y:1500 , ASP Y:1503 , HIS Y:1505 , ASP Y:1507 , ASP Y:1518 , ASP Y:1521
BINDING SITE FOR RESIDUE CA Y 2002
9
AC9
SOFTWARE
HIS Y:1540 , ASP Y:1543 , HIS Y:1545 , ASP Y:1547 , ASP Y:1558 , ASP Y:1561
BINDING SITE FOR RESIDUE CA Y 2003
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SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_071961 (C1497Y, chain X/Y, )
2: VAR_046618 (V1672I, chain X/Y, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_071961
C
1496
Y
NOTC1_HUMAN
Disease (AOS5)
---
X/Y
C
1497
Y
2
UniProt
VAR_046618
V
1671
I
NOTC1_HUMAN
Polymorphism
2229968
X/Y
V
1672
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 5)
Info
All PROSITE Patterns/Profiles
1: LNR (Y:1533-1572)
;
View:
Select:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LNR
PS50258
LNR (Lin-12/Notch) repeat profile.
NOTC1_HUMAN
1449-1489
1490-1531
1532-1571
5
X:1450-1490
X:1491-1532
Y:1491-1532
X:1533-1572
Y:1533-1572
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_3l95A02 (A:109-212)
1b: CATH_3l95B02 (B:114-214)
1c: CATH_3l95H02 (H:114-213)
1d: CATH_3l95B01 (B:1-113)
1e: CATH_3l95H01 (H:1-113)
1f: CATH_3l95L02 (L:109-212)
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(
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(
)
(
)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
[unclassified]
(54)
1a
3l95A02
A:109-212
1b
3l95B02
B:114-214
1c
3l95H02
H:114-213
1d
3l95B01
B:1-113
1e
3l95H01
H:1-113
1f
3l95L02
L:109-212
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Pfam Domains
(3, 10)
Info
all PFAM domains
1a: PFAM_NODP_3l95Y01 (Y:1671-1726)
1b: PFAM_NODP_3l95Y02 (Y:1671-1726)
2a: PFAM_NOD_3l95Y03 (Y:1567-1622)
2b: PFAM_NOD_3l95Y04 (Y:1567-1622)
3a: PFAM_Notch_3l95Y05 (Y:1527-1563)
3b: PFAM_Notch_3l95Y06 (Y:1527-1563)
3c: PFAM_Notch_3l95Y07 (Y:1527-1563)
3d: PFAM_Notch_3l95Y08 (Y:1527-1563)
3e: PFAM_Notch_3l95Y09 (Y:1527-1563)
3f: PFAM_Notch_3l95Y10 (Y:1527-1563)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: NODP]
(2)
Family
:
NODP
(2)
Homo sapiens (Human)
(2)
1a
NODP-3l95Y01
Y:1671-1726
1b
NODP-3l95Y02
Y:1671-1726
Clan
:
no clan defined [family: NOD]
(2)
Family
:
NOD
(2)
Homo sapiens (Human)
(2)
2a
NOD-3l95Y03
Y:1567-1622
2b
NOD-3l95Y04
Y:1567-1622
Clan
:
no clan defined [family: Notch]
(3)
Family
:
Notch
(3)
Homo sapiens (Human)
(3)
3a
Notch-3l95Y05
Y:1527-1563
3b
Notch-3l95Y06
Y:1527-1563
3c
Notch-3l95Y07
Y:1527-1563
3d
Notch-3l95Y08
Y:1527-1563
3e
Notch-3l95Y09
Y:1527-1563
3f
Notch-3l95Y10
Y:1527-1563
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Asym.Unit (216 KB)
Header - Asym.Unit
Biol.Unit 1 (174 KB)
Header - Biol.Unit 1
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