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3UPC
Asym. Unit
Info
Asym.Unit (337 KB)
Biol.Unit 1 (37 KB)
Biol.Unit 10 (35 KB)
Biol.Unit 11 (70 KB)
Biol.Unit 12 (69 KB)
Biol.Unit 13 (67 KB)
Biol.Unit 14 (68 KB)
Biol.Unit 15 (69 KB)
Biol.Unit 2 (36 KB)
Biol.Unit 3 (36 KB)
Biol.Unit 4 (36 KB)
Biol.Unit 5 (34 KB)
Biol.Unit 6 (36 KB)
Biol.Unit 7 (37 KB)
Biol.Unit 8 (36 KB)
Biol.Unit 9 (36 KB)
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(1)
Title
:
A GENERAL STRATEGY FOR THE GENERATION OF HUMAN ANTIBODY VARIABLE DOMAINS WITH INCREASED AGGREGATION RESISTANCE
Authors
:
K. Dudgeon, R. Rouet, I. Kokmeijer, D. B. Langley, D. Christ
Date
:
17 Nov 11 (Deposition) - 20 Jun 12 (Release) - 15 Aug 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Biol. Unit 9: I (1x)
Biol. Unit 10: J (1x)
Biol. Unit 11: A,B (1x)
Biol. Unit 12: C,D (1x)
Biol. Unit 13: E,I (1x)
Biol. Unit 14: F,J (1x)
Biol. Unit 15: G,H (1x)
Keywords
:
Immunoglobulin Fold, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Dudgeon, R. Rouet, I. Kokmeijer, P. Schofield, J. Stolp, D. Langley D. Stock, D. Christ
General Strategy For The Generation Of Human Antibody Variable Domains With Increased Aggregation Resistance
Proc. Natl. Acad. Sci. Usa V. 109 10879 2012
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Hetero Components
(4, 7)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
2a: DI(HYDROXYETHYL)ETHER (PEGa)
3a: TETRAETHYLENE GLYCOL (PG4a)
3b: TETRAETHYLENE GLYCOL (PG4b)
3c: TETRAETHYLENE GLYCOL (PG4c)
4a: TRIETHYLENE GLYCOL (PGEa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
2
Ligand/Ion
PENTAETHYLENE GLYCOL
2
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
3
PG4
3
Ligand/Ion
TETRAETHYLENE GLYCOL
4
PGE
1
Ligand/Ion
TRIETHYLENE GLYCOL
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:35 , VAL A:37 , TRP A:47 , TRP A:106
BINDING SITE FOR RESIDUE 1PE A 2
2
AC2
SOFTWARE
PEG C:116 , TYR D:100 , TRP D:106
BINDING SITE FOR RESIDUE 1PE D 116
3
AC3
SOFTWARE
PG4 G:116 , TRP H:47 , TYR H:100 , TRP H:106
BINDING SITE FOR RESIDUE PG4 H 1
4
AC4
SOFTWARE
TYR G:105 , TRP G:106 , PG4 H:1
BINDING SITE FOR RESIDUE PG4 G 116
5
AC5
SOFTWARE
TRP I:47 , TYR I:100 , TYR I:105 , TRP I:106
BINDING SITE FOR RESIDUE PG4 I 116
6
AC6
SOFTWARE
TRP B:47 , TYR B:100 , TRP B:106 , PEG C:116
BINDING SITE FOR RESIDUE PGE B 116
7
AC7
SOFTWARE
PGE B:116 , TRP C:47 , TYR C:100 , TRP C:106 , 1PE D:116
BINDING SITE FOR RESIDUE PEG C 116
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SAPs(SNPs)/Variants
(2, 20)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_073326 (L5L, chain A/B/C/D/E/F/G/H/I/J, )
2: VAR_073327 (A61G, chain A/B/C/D/E/F/G/H/I/J, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_073326
V
24
L
HV303_HUMAN
Polymorphism
---
A/B/C/D/E/F/G/H/I/J
L
5
L
2
UniProt
VAR_073327
A
80
G
HV303_HUMAN
Polymorphism
---
A/B/C/D/E/F/G/H/I/J
A
61
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
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Exons
(1, 10)
Info
All Exons
Exon 1.2 (A:3-97 | B:3-97 | C:3-97 | D:3-97 ...)
View:
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Label:
All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/-
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
1.1
ENST00000390609
1
ENSE00002048341
chr14:
106725733-106725609
125
HV323_HUMAN
1-16
16
0
-
-
1.2
ENST00000390609
2
ENSE00001851371
chr14:
106725505-106725201
305
HV323_HUMAN
16-116
101
10
A:3-97
B:3-97
C:3-97
D:3-97
E:3-97
F:3-97
G:3-97
H:3-97
I:3-97
J:3-97
95
95
95
95
95
95
95
95
95
95
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SCOP Domains
(1, 10)
Info
All SCOP Domains
1a: SCOP_d3upca_ (A:)
1b: SCOP_d3upcb_ (B:)
1c: SCOP_d3upcc_ (C:)
1d: SCOP_d3upcd_ (D:)
1e: SCOP_d3upce_ (E:)
1f: SCOP_d3upcf_ (F:)
1g: SCOP_d3upcg_ (G:)
1h: SCOP_d3upch_ (H:)
1i: SCOP_d3upci_ (I:)
1j: SCOP_d3upcj_ (J:)
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Protein Domains
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Organisms
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(
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Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
automated matches
(311)
Human (Homo sapiens) [TaxId: 9606]
(85)
1a
d3upca_
A:
1b
d3upcb_
B:
1c
d3upcc_
C:
1d
d3upcd_
D:
1e
d3upce_
E:
1f
d3upcf_
F:
1g
d3upcg_
G:
1h
d3upch_
H:
1i
d3upci_
I:
1j
d3upcj_
J:
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Chain E
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Chain H
Chain I
Chain J
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
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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") .
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Show PDB file:
Asym.Unit (337 KB)
Header - Asym.Unit
Biol.Unit 1 (37 KB)
Header - Biol.Unit 1
Biol.Unit 10 (35 KB)
Header - Biol.Unit 10
Biol.Unit 11 (70 KB)
Header - Biol.Unit 11
Biol.Unit 12 (69 KB)
Header - Biol.Unit 12
Biol.Unit 13 (67 KB)
Header - Biol.Unit 13
Biol.Unit 14 (68 KB)
Header - Biol.Unit 14
Biol.Unit 15 (69 KB)
Header - Biol.Unit 15
Biol.Unit 2 (36 KB)
Header - Biol.Unit 2
Biol.Unit 3 (36 KB)
Header - Biol.Unit 3
Biol.Unit 4 (36 KB)
Header - Biol.Unit 4
Biol.Unit 5 (34 KB)
Header - Biol.Unit 5
Biol.Unit 6 (36 KB)
Header - Biol.Unit 6
Biol.Unit 7 (37 KB)
Header - Biol.Unit 7
Biol.Unit 8 (36 KB)
Header - Biol.Unit 8
Biol.Unit 9 (36 KB)
Header - Biol.Unit 9
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