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1OP5
Asym. Unit
Info
Asym.Unit (151 KB)
Biol.Unit 1 (139 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF FAB 2G12 BOUND TO MAN9GLCNAC2
Authors
:
D. A. Calarese, C. N. Scanlan, M. B. Zwick, S. Deechongkit, Y. Mimura, R. R. L. Stanfield, J. W. Kelly, P. M. Rudd, R. A. Dwek, H. Katinger, D. R. Bu I. A. Wilson
Date
:
04 Mar 03 (Deposition) - 15 Jul 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : H,K,L,M
Biol. Unit 1: H,K,L,M (1x)
Keywords
:
Domain-Swapped Fab 2G12 Man9Glcnac2 Anti-Carbohydrate Antibody, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. A. Calarese, C. N. Scanlan, M. B. Zwick, S. Deechongkit, Y. Mimura, R. Kunert, P. Zhu, M. R. Wormald, R. L. Stanfield, K. H. Roux, J. W. Kelly P. M. Rudd, R. A. Dwek, H. Katinger, D. R. Burton, I. A. Wilson
Antibody Domain Exchange Is An Immunological Solution To Carbohydrate Cluster Recognition.
Science V. 300 2065 2003
[
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Hetero Components
(3, 22)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
2c: ALPHA-D-MANNOSE (MANc)
2d: ALPHA-D-MANNOSE (MANd)
2e: ALPHA-D-MANNOSE (MANe)
2f: ALPHA-D-MANNOSE (MANf)
2g: ALPHA-D-MANNOSE (MANg)
2h: ALPHA-D-MANNOSE (MANh)
2i: ALPHA-D-MANNOSE (MANi)
2j: ALPHA-D-MANNOSE (MANj)
2k: ALPHA-D-MANNOSE (MANk)
2l: ALPHA-D-MANNOSE (MANl)
2m: ALPHA-D-MANNOSE (MANm)
2n: ALPHA-D-MANNOSE (MANn)
2o: ALPHA-D-MANNOSE (MANo)
2p: ALPHA-D-MANNOSE (MANp)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
MAN
16
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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]
Sites
(22, 22)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
NAG H:230 , NAG K:215
BINDING SITE FOR RESIDUE NAG K 214
02
AC2
SOFTWARE
LEU H:74 , NAG K:214 , BMA K:216
BINDING SITE FOR RESIDUE NAG K 215
03
AC3
SOFTWARE
NAG K:215 , MAN K:217 , MAN K:218 , ASP M:100B
BINDING SITE FOR RESIDUE BMA K 216
04
AC4
SOFTWARE
TYR K:94 , BMA K:216 , THR M:52A , ASP M:100B , MAN M:230
BINDING SITE FOR RESIDUE MAN K 217
05
AC5
SOFTWARE
LEU H:74 , BMA K:216 , MAN K:219 , MAN M:232
BINDING SITE FOR RESIDUE MAN K 218
06
AC6
SOFTWARE
MAN K:218 , MAN M:234
BINDING SITE FOR RESIDUE MAN K 219
07
AC7
SOFTWARE
MAN K:217 , ALA M:31 , THR M:52A , ASP M:100B , MAN M:231
BINDING SITE FOR RESIDUE MAN M 230
08
AC8
SOFTWARE
GLY K:93 , TYR K:94 , ALA M:31 , HIS M:32 , THR M:33 , THR M:52A , LYS M:95 , GLY M:96 , SER M:100A , ASP M:100B , ASN M:100C , ASP M:100D , MAN M:230
BINDING SITE FOR RESIDUE MAN M 231
09
AC9
SOFTWARE
LEU H:74 , GLU H:75 , MAN K:218 , SER M:54 , ARG M:57 , MAN M:233
BINDING SITE FOR RESIDUE MAN M 232
10
BC1
SOFTWARE
THR M:55 , TYR M:56 , ARG M:57 , MAN M:232
BINDING SITE FOR RESIDUE MAN M 233
11
BC2
SOFTWARE
ARG H:28 , MAN K:219
BINDING SITE FOR RESIDUE MAN M 234
12
BC3
SOFTWARE
NAG H:231 , NAG K:214
BINDING SITE FOR RESIDUE NAG H 230
13
BC4
SOFTWARE
NAG H:230 , BMA H:232 , LEU M:74
BINDING SITE FOR RESIDUE NAG H 231
14
BC5
SOFTWARE
ASP H:100B , NAG H:231 , MAN H:233 , MAN H:234
BINDING SITE FOR RESIDUE BMA H 232
15
BC6
SOFTWARE
ASP H:100B , BMA H:232 , MAN H:237 , TYR L:94
BINDING SITE FOR RESIDUE MAN H 233
16
BC7
SOFTWARE
ASP H:100B , BMA H:232 , MAN H:235 , MAN H:236 , MAN L:214 , LEU M:74
BINDING SITE FOR RESIDUE MAN H 234
17
BC8
SOFTWARE
MAN H:234 , MAN H:236
BINDING SITE FOR RESIDUE MAN H 235
18
BC9
SOFTWARE
MAN H:234 , MAN H:235
BINDING SITE FOR RESIDUE MAN H 236
19
CC1
SOFTWARE
ALA H:31 , MAN H:233 , MAN H:238
BINDING SITE FOR RESIDUE MAN H 237
20
CC2
SOFTWARE
ALA H:31 , HIS H:32 , THR H:33 , THR H:52A , LYS H:95 , GLY H:96 , LEU H:100 , SER H:100A , ASP H:100B , ASN H:100C , ASP H:100D , MAN H:237 , GLY L:93 , TYR L:94
BINDING SITE FOR RESIDUE MAN H 238
21
CC3
SOFTWARE
SER H:54 , THR H:55 , ARG H:57 , MAN H:234 , MAN L:215 , LEU M:74 , GLU M:75
BINDING SITE FOR RESIDUE MAN L 214
22
CC4
SOFTWARE
ARG H:57 , TYR L:94 , MAN L:214
BINDING SITE FOR RESIDUE MAN L 215
[
close Site info
]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_066403 (W148R, chain K/L, )
2: VAR_003897 (V191L, chain K/L, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_066403
W
40
R
IGKC_HUMAN
Disease (IGKCD)
---
K/L
W
148
R
2
UniProt
VAR_003897
V
83
L
IGKC_HUMAN
Unclassified
---
K/L
V
191
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (K:192-198,L:192-198)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
IGKC_HUMAN
85-91
2
K:192-198
L:192-198
[
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Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d1op5h2 (H:116-229)
1b: SCOP_d1op5m2 (M:116-229)
2a: SCOP_d1op5k2 (K:108-213)
2b: SCOP_d1op5l2 (L:108-213)
3a: SCOP_d1op5h1 (H:1-115)
3b: SCOP_d1op5m1 (M:1-115)
4a: SCOP_d1op5k1 (K:2-107)
4b: SCOP_d1op5l1 (L:2-107)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma
(608)
Human (Homo sapiens) [TaxId: 9606]
(179)
1a
d1op5h2
H:116-229
1b
d1op5m2
M:116-229
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d1op5k2
K:108-213
2b
d1op5l2
L:108-213
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Engineered (including hybrid species)
(68)
3a
d1op5h1
H:1-115
3b
d1op5m1
M:1-115
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Engineered (including hybrid species)
(61)
4a
d1op5k1
K:2-107
4b
d1op5l1
L:2-107
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1op5K02 (K:109-208)
1b: CATH_1op5H02 (H:114-226)
1c: CATH_1op5M02 (M:114-226)
1d: CATH_1op5H01 (H:1-113)
1e: CATH_1op5M01 (M:1-113)
1f: CATH_1op5L02 (L:108-211)
1g: CATH_1op5L01 (L:2-107)
1h: CATH_1op5K01 (K:2-108)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
1op5K02
K:109-208
1b
1op5H02
H:114-226
1c
1op5M02
M:114-226
1d
1op5H01
H:1-113
1e
1op5M01
M:1-113
1f
1op5L02
L:108-211
1g
1op5L01
L:2-107
1h
1op5K01
K:2-108
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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