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1LGB
Asym. Unit
Info
Asym.Unit (72 KB)
Biol.Unit 1 (128 KB)
Biol.Unit 2 (66 KB)
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(1)
Title
:
INTERACTION OF A LEGUME LECTIN WITH THE N2 FRAGMENT OF HUMAN LACTOTRANSFERRIN OR WITH THE ISOLATED BIANTENNARY GLYCOPEPTIDE: ROLE OF THE FUCOSE MOIETY
Authors
:
Y. Bourne, C. Cambillau
Date
:
07 Jan 94 (Deposition) - 31 Aug 94 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (2x)
Biol. Unit 2: A,B,C (1x)
Keywords
:
Complex(Lectin-Transferrin), Complex(Lectin-Transferrin) Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Bourne, J. Mazurier, D. Legrand, P. Rouge, J. Montreuil, G. Spik, C. Cambillau
Structures Of A Legume Lectin Complexed With The Human Lactotransferrin N2 Fragment, And With An Isolated Biantennary Glycopeptide: Role Of The Fucose Moiety.
Structure V. 2 209 1994
(for further references see the
PDB file header
)
[
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]
Hetero Components
(7, 11)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: CALCIUM ION (CAa)
3a: ALPHA-L-FUCOSE (FUCa)
4a: BETA-D-GALACTOSE (GALa)
5a: ALPHA-D-MANNOSE (MANa)
5b: ALPHA-D-MANNOSE (MANb)
6a: MANGANESE (II) ION (MNa)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
CA
1
Ligand/Ion
CALCIUM ION
3
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
4
GAL
1
Ligand/Ion
BETA-D-GALACTOSE
5
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
6
MN
1
Ligand/Ion
MANGANESE (II) ION
7
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(13, 13)
Info
All Sites
01: A (AUTHOR)
02: AC1 (SOFTWARE)
03: AC2 (SOFTWARE)
04: AC3 (SOFTWARE)
05: AC4 (SOFTWARE)
06: AC5 (SOFTWARE)
07: AC6 (SOFTWARE)
08: AC7 (SOFTWARE)
09: AC8 (SOFTWARE)
10: AC9 (SOFTWARE)
11: B (AUTHOR)
12: BC1 (SOFTWARE)
13: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
A
AUTHOR
GLY A:99 , ASP A:81 , ASN A:125 , GLY B:29 , ALA B:30 , GLU B:31
MANNOSE BINDING SITE
02
AC1
SOFTWARE
ASP A:81 , GLY A:99 , PHE A:123 , ASN A:125 , GLY B:29 , ALA B:30 , GLU B:31 , BMA C:502 , NAG C:505
BINDING SITE FOR RESIDUE MAN C 501
03
AC2
SOFTWARE
PHE A:123 , MAN C:501 , MAN C:503 , NAG C:508
BINDING SITE FOR RESIDUE BMA C 502
04
AC3
SOFTWARE
BMA C:502 , NAG C:504
BINDING SITE FOR RESIDUE MAN C 503
05
AC4
SOFTWARE
MAN C:503
BINDING SITE FOR RESIDUE NAG C 504
06
AC5
SOFTWARE
ASN A:39 , MAN C:501 , GAL C:507
BINDING SITE FOR RESIDUE NAG C 505
07
AC6
SOFTWARE
NAG C:505
BINDING SITE FOR RESIDUE GAL C 507
08
AC7
SOFTWARE
ALA B:30 , GLU B:31 , BMA C:502 , NAG C:509 , FUC C:510
BINDING SITE FOR RESIDUE NAG C 508
09
AC8
SOFTWARE
TYR A:77 , ASN A:78 , GLN C:110 , PHE C:135 , ASN C:137 , NAG C:508 , FUC C:510
BINDING SITE FOR RESIDUE NAG C 509
10
AC9
SOFTWARE
TYR A:77 , PHE A:123 , GLU B:31 , NAG C:508 , NAG C:509
BINDING SITE FOR RESIDUE FUC C 510
11
B
AUTHOR
PHE B:32 , GLU B:31
FUCOSE BINDING CAVITY
12
BC1
SOFTWARE
GLU A:119 , ASP A:129 , HIS A:136
BINDING SITE FOR RESIDUE MN A 300
13
BC2
SOFTWARE
ASP A:81 , ASP A:121 , PHE A:123 , ASN A:125 , ASP A:129
BINDING SITE FOR RESIDUE CA A 301
[
close Site info
]
SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_LECB_LATOC_001 (P16P, chain A, )
2: VAR_LECB_LATOC_002 (S66A, chain A, )
3: VAR_013506 (I129T, chain C, )
4: VAR_LECB_LATOC_003 (G168G, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_LECB_LATOC_001
*
Q
16
P
LECB_LATOC
---
---
A
P
16
P
2
UniProt
VAR_LECB_LATOC_002
*
S
66
A
LECB_LATOC
---
---
A
S
66
A
3
UniProt
VAR_013506
I
148
T
TRFL_HUMAN
Polymorphism
1126479
C
I
129
T
4
UniProt
VAR_LECB_LATOC_003
*
A
168
G
LECB_LATOC
---
---
A
G
168
G
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(5, 5)
Info
All PROSITE Patterns/Profiles
1: LECTIN_LEGUME_ALPHA (B:16-25)
2: TRANSFERRIN_LIKE_1 (C:92-101|-)
3: LECTIN_LEGUME_BETA (A:116-122)
4: TRANSFERRIN_LIKE_2 (C:192-208|-)
5: TRANSFERRIN_LIKE_3 (C:226-249|-)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LECTIN_LEGUME_ALPHA
PS00308
Legume lectins alpha-chain signature.
LEC2_LATOC
16-25
1
B:16-25
2
TRANSFERRIN_LIKE_1
PS00205
Transferrin-like domain signature 1.
TRFL_HUMAN
111-120
454-463
1
C:92-101
-
3
LECTIN_LEGUME_BETA
PS00307
Legume lectins beta-chain signature.
LECB_LATOC
116-122
1
A:116-122
4
TRANSFERRIN_LIKE_2
PS00206
Transferrin-like domain signature 2.
TRFL_HUMAN
211-227
547-563
1
C:192-208
-
5
TRANSFERRIN_LIKE_3
PS00207
Transferrin-like domain signature 3.
TRFL_HUMAN
245-275
589-619
1
C:226-249
-
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.10a (C:91-148)
Exon 1.12b (C:148-197)
Exon 1.13a (C:197-216)
Exon 1.14 (C:216-249)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.9/1.10a
2: Boundary 1.10a/1.12b
3: Boundary 1.12b/1.13a
4: Boundary 1.13a/1.14
5: Boundary 1.14/1.15
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
1.5a
ENST00000231751
5a
ENSE00001814982
chr3:
46506653-46506315
339
TRFL_HUMAN
1-15
15
0
-
-
1.8b
ENST00000231751
8b
ENSE00001591766
chr3:
46501309-46501146
164
TRFL_HUMAN
15-69
55
0
-
-
1.9
ENST00000231751
9
ENSE00001078630
chr3:
46497888-46497780
109
TRFL_HUMAN
70-106
37
0
-
-
1.10a
ENST00000231751
10a
ENSE00002201536
chr3:
46497468-46497286
183
TRFL_HUMAN
106-167
62
1
C:91-148
58
1.12b
ENST00000231751
12b
ENSE00001078629
chr3:
46496932-46496785
148
TRFL_HUMAN
167-216
50
1
C:148-197
50
1.13a
ENST00000231751
13a
ENSE00000825947
chr3:
46495850-46495795
56
TRFL_HUMAN
216-235
20
1
C:197-216
20
1.14
ENST00000231751
14
ENSE00000825946
chr3:
46492163-46491985
179
TRFL_HUMAN
235-294
60
1
C:216-249
34
1.15
ENST00000231751
15
ENSE00000767141
chr3:
46491518-46491344
175
TRFL_HUMAN
295-353
59
0
-
-
1.16b
ENST00000231751
16b
ENSE00000767140
chr3:
46490508-46490354
155
TRFL_HUMAN
353-404
52
0
-
-
1.17
ENST00000231751
17
ENSE00000492524
chr3:
46488889-46488799
91
TRFL_HUMAN
405-435
31
0
-
-
1.18
ENST00000231751
18
ENSE00000767138
chr3:
46487984-46487931
54
TRFL_HUMAN
435-453
19
0
-
-
1.19
ENST00000231751
19
ENSE00000492526
chr3:
46486927-46486772
156
TRFL_HUMAN
453-505
53
0
-
-
1.20
ENST00000231751
20
ENSE00000492527
chr3:
46485073-46484932
142
TRFL_HUMAN
505-552
48
0
-
-
1.22a
ENST00000231751
22a
ENSE00000767135
chr3:
46482974-46482907
68
TRFL_HUMAN
552-575
24
0
-
-
1.23a
ENST00000231751
23a
ENSE00001292001
chr3:
46480971-46480787
185
TRFL_HUMAN
575-636
62
0
-
-
1.24c
ENST00000231751
24c
ENSE00000825945
chr3:
46479620-46479431
190
TRFL_HUMAN
637-700
64
0
-
-
1.25c
ENST00000231751
25c
ENSE00001289842
chr3:
46477720-46477136
585
TRFL_HUMAN
700-710
11
0
-
-
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1lgb_1 (A:,B:)
2a: SCOP_d1lgbc_ (C:)
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(
)
(
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Folds
(
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(
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(
)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Concanavalin A-like lectins/glucanases
(797)
Superfamily
:
Concanavalin A-like lectins/glucanases
(797)
Family
:
Legume lectins
(238)
Protein domain
:
Legume lectin
(110)
Lathyrus ochrus, isolectin II [TaxId: 3858]
(2)
1a
d1lgb.1
A:,B:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Periplasmic binding protein-like II
(813)
Superfamily
:
Periplasmic binding protein-like II
(813)
Family
:
Transferrin
(82)
Protein domain
:
Lactoferrin
(42)
Human (Homo sapiens) [TaxId: 9606]
(22)
2a
d1lgbc_
C:
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1lgbC00 (C:91-249)
2a: CATH_1lgbA00 (A:1-181)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
D-Maltodextrin-Binding Protein; domain 2
(600)
Homologous Superfamily
:
Periplasmic binding protein-like II
(486)
Yellow-flowered pea (Lathyrus ochruss)
(1)
1a
1lgbC00
C:91-249
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.200, no name defined]
(421)
Yellow-flowered pea (Lathyrus ochruss)
(1)
2a
1lgbA00
A:1-181
[
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Pfam Domains
(2, 3)
Info
all PFAM domains
1a: PFAM_Lectin_legB_1lgbB01 (B:2-43)
1b: PFAM_Lectin_legB_1lgbA01 (A:2-181)
2a: PFAM_Transferrin_1lgbC01 (C:91-249)
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Clans
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Families
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(
)
Organisms
(
)
(
)
Clan
:
Concanavalin
(293)
Family
:
Lectin_legB
(93)
Lathyrus ochrus (Yellow-flowered pea)
(6)
1a
Lectin_legB-1lgbB01
B:2-43
1b
Lectin_legB-1lgbA01
A:2-181
Clan
:
PBP
(391)
Family
:
Transferrin
(53)
Homo sapiens (Human)
(23)
2a
Transferrin-1lgbC01
C:91-249
[
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Asym.Unit (72 KB)
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Header - Biol.Unit 1
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