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Numbering & Regions

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Region Sequence Details
Regions Definition:
Region Sequence Fragment Residues Length
LFR1
DIVLTQSPGSLAVSLGQRATISC
1 - 23 23
CDR-L1
RASESVDDDGNSFLH
24 - 38 15
LFR2
WYQQKPGQPPKLLIY
39 - 53 15
CDR-L2
RSSNLIS
54 - 60 7
LFR3
GIPDRFSGSGSRTDFTLTINPVEADDVATYYC
61 - 92 32
CDR-L3
QQSNEDPLT
93 - 101 9
LFR4
FGAGTKLEIKRA
102 - 113 12
Tail
DAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSK
DSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
114 - 218 105
218
Region Sequence Fragment Residues Length
LFR1
DIVLTQSPGSLAVSLGQRATISC
1 - 23 23
CDR-L1
RASESVDDDGNSFLH
24 - 38 15
LFR2
WYQQKPGQPPKLLIY
39 - 53 15
CDR-L2
RSSNLIS
54 - 60 7
LFR3
GIPDRFSGSGSRTDFTLTINPVEADDVATYYC
61 - 92 32
CDR-L3
QQSNEDPLT
93 - 101 9
LFR4
FGAGTKLEIKRA
102 - 113 12
Tail
DAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSK
DSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
114 - 218 105
218
Region Sequence Fragment Residues Length
LFR1
DIVLTQSPGSLAVSLGQRATISC
1 - 23 23
CDR-L1
RASESVDDDGNSFLH
24 - 38 15
LFR2
WYQQKPGQPPKLLIY
39 - 53 15
CDR-L2
RSSNLIS
54 - 60 7
LFR3
GIPDRFSGSGSRTDFTLTINPVEADDVATYYC
61 - 92 32
CDR-L3
QQSNEDPLT
93 - 101 9
LFR4
FGAGTKLEIKRA
102 - 113 12
Tail
DAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSK
DSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
114 - 218 105
218
Region Sequence Fragment Residues Length
LFR1
DIVLTQSPGSLAVSLGQRATISCRASESV
1 - 29 29
CDR-L1
DDDGNSFLHWY
30 - 40 11
LFR2
QQKPGQPPK
41 - 49 9
CDR-L2
LLIYRSSNLI
50 - 59 10
LFR3
SGIPDRFSGSGSRTDFTLTINPVEADDVATYYC
60 - 92 33
CDR-L3
QQSNEDPL
93 - 100 8
LFR4
TFGAGTKLEIKRA
101 - 113 13
Tail
DAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSK
DSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
114 - 218 105
218
Region Sequence Fragment Residues Length
LFR1
DIVLTQSPGSLAVSLGQRATISCRAS
1 - 26 26
CDR-L1
ESVDDDGNSF
27 - 36 10
LFR2
LHWYQQKPGQPPKLLIY
37 - 53 17
CDR-L2
RS
54 - 55 2
LFR3
SNLISGIPDRFSGSGSRTDFTLTINPVEADDVATYYC
56 - 92 37
CDR-L3
QQSNEDPLT
93 - 101 9
LFR4
FGAGTKLEIKRA
102 - 113 12
Tail
DAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSK
DSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
114 - 218 105
218
Region Definition Sequence Fragment Residues Length
LFR1 Chothia
DIVLTQSPGSLAVSLGQRATISC------
1 - 23 23
AbM
DIVLTQSPGSLAVSLGQRATISC------
1 - 23 23
Kabat
DIVLTQSPGSLAVSLGQRATISC------
1 - 23 23
Contact
DIVLTQSPGSLAVSLGQRATISCRASESV
1 - 29 29
IMGT
DIVLTQSPGSLAVSLGQRATISCRAS---
1 - 26 26
CDR-L1 Chothia
RASESVDDDGNSFLH--
24 - 38 15
AbM
RASESVDDDGNSFLH--
24 - 38 15
Kabat
RASESVDDDGNSFLH--
24 - 38 15
Contact
------DDDGNSFLHWY
30 - 40 11
IMGT
---ESVDDDGNSF----
27 - 36 10
LFR2 Chothia
--WYQQKPGQPPKLLIY
39 - 53 15
AbM
--WYQQKPGQPPKLLIY
39 - 53 15
Kabat
--WYQQKPGQPPKLLIY
39 - 53 15
Contact
----QQKPGQPPK----
41 - 49 9
IMGT
LHWYQQKPGQPPKLLIY
37 - 53 17
CDR-L2 Chothia
----RSSNLIS
54 - 60 7
AbM
----RSSNLIS
54 - 60 7
Kabat
----RSSNLIS
54 - 60 7
Contact
LLIYRSSNLI-
50 - 59 10
IMGT
----RS-----
54 - 55 2
LFR3 Chothia
-----GIPDRFSGSGSRTDFTLTINPVEADDVATYYC
61 - 92 32
AbM
-----GIPDRFSGSGSRTDFTLTINPVEADDVATYYC
61 - 92 32
Kabat
-----GIPDRFSGSGSRTDFTLTINPVEADDVATYYC
61 - 92 32
Contact
----SGIPDRFSGSGSRTDFTLTINPVEADDVATYYC
60 - 92 33
IMGT
SNLISGIPDRFSGSGSRTDFTLTINPVEADDVATYYC
56 - 92 37
CDR-L3 Chothia
QQSNEDPLT
93 - 101 9
AbM
QQSNEDPLT
93 - 101 9
Kabat
QQSNEDPLT
93 - 101 9
Contact
QQSNEDPL-
93 - 100 8
IMGT
QQSNEDPLT
93 - 101 9
LFR4 Chothia
-FGAGTKLEIKRA
102 - 113 12
AbM
-FGAGTKLEIKRA
102 - 113 12
Kabat
-FGAGTKLEIKRA
102 - 113 12
Contact
TFGAGTKLEIKRA
101 - 113 13
IMGT
-FGAGTKLEIKRA
102 - 113 12
Humanness

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Accession & Annotations
Accession 1ggi_M
Source PDB  1ggi  Submitted 02-APR-1993  Updated 25-AUG-2009
Name
CRYSTAL STRUCTURE OF AN HIV-1 NEUTRALIZING ANTIBODY 50.1 IN COMPLEX WITH ITS V3 LOOP PEPTIDE ANTIGEN
Organism
Mus musculus
Chain Type Light
Pairing 1ggi_J
Identical Protein Sequences PDB: 1ggi_L
References
RINI M., STANFIELD L., STURA A., SALINAS A., PROFY T., WILSON A.
'CRYSTAL STRUCTURE OF A HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 NEUTRALIZING ANTIBODY, 50.1, IN COMPLEX WITH ITS V3 LOOP PEPTIDE ANTIGEN.'
PROC.NATL.ACAD.SCI.USA V. 90 6325 1993 ISSN 0027-8424
Sequences
Amino Acid Sequence:
DIVLTQSPGSLAVSLGQRATISCRASESVDDDGNSFLHWYQQKPGQPPKLLIYRSSNLIS
GIPDRFSGSGSRTDFTLTINPVEADDVATYYCQQSNEDPLTFGAGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

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Germline Tools
Data Source:
Data Source V D J Exclude if warnings
NCBI Germline
V-BASE
Alignment settings:
Rank alignments by
Exclude identical hits
Search settings:
V-segment score threshold
D-segment score threshold
J-segment score threshold
Gaps:
Gap penalty

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abYmod homology modelling

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Chains
1ggi_J
All Heavy
All HFR
All CDR-H
HFR1
CDR-H1
HFR2
CDR-H2
HFR3
CDR-H3
HFR4
Other Heavy
1ggi_M
All Light
All LFR
All CDR-L
LFR1
CDR-L1
LFR2
CDR-L2
LFR3
CDR-L3
LFR4
Other Light
Colours
Labels
On
Off
Atoms
Main chain
All
Style
Wireframe
Ball and Stick
Spacefill
Cartoon
Backbone
Reset
Black
Reset
White

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