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1V6N
Asym. Unit
Info
Asym.Unit (264 KB)
Biol.Unit 1 (131 KB)
Biol.Unit 2 (131 KB)
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(1)
Title
:
PEANUT LECTIN WITH 9MER PEPTIDE (PVIWSSATG)
Authors
:
S. Kundhavai Natchiar, A. Arockia Jeyaprakash, T. N. C. Ramya, C. J. Thomas, K. Suguna, A. Surolia, M. Vijayan
Date
:
02 Dec 03 (Deposition) - 10 Feb 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Lectin, Agglutinin, Open Quaternary Association, Peptide And Monoclinic, Sugar Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Kundhavai Natchiar, A. Arockia Jeyaprakash, T. N. Ramya, C. J. Thomas, K. Suguna, A. Surolia, M. Vijayan
Structural Plasticity Of Peanut Lectin: An X-Ray Analysis Involving Variation In Ph, Ligand Binding And Crystal Structure.
Acta Crystallogr. , Sect. D V. 60 211 2004
(for further references see the
PDB file header
)
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Hetero Components
(2, 16)
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)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
2e: MANGANESE (II) ION (MNe)
2f: MANGANESE (II) ION (MNf)
2g: MANGANESE (II) ION (MNg)
2h: MANGANESE (II) ION (MNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
8
Ligand/Ion
CALCIUM ION
2
MN
8
Ligand/Ion
MANGANESE (II) ION
[
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Sites
(16, 16)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:123 , TYR A:125 , ASN A:127 , ASP A:132
BINDING SITE FOR RESIDUE CA A 1237
02
AC2
SOFTWARE
GLU A:121 , ASP A:123 , ASP A:132 , HIS A:137
BINDING SITE FOR RESIDUE MN A 1238
03
AC3
SOFTWARE
ASP B:123 , TYR B:125 , ASN B:127 , ASP B:132
BINDING SITE FOR RESIDUE CA B 2237
04
AC4
SOFTWARE
GLU B:121 , ASP B:123 , ASP B:132 , HIS B:137 , SER B:147
BINDING SITE FOR RESIDUE MN B 2238
05
AC5
SOFTWARE
ASP C:123 , TYR C:125 , ASN C:127 , ASP C:132
BINDING SITE FOR RESIDUE CA C 3237
06
AC6
SOFTWARE
GLU C:121 , ASP C:123 , ASP C:132 , HIS C:137 , VAL C:145
BINDING SITE FOR RESIDUE MN C 3238
07
AC7
SOFTWARE
ASP D:123 , TYR D:125 , ASN D:127 , ASP D:132
BINDING SITE FOR RESIDUE CA D 4237
08
AC8
SOFTWARE
GLU D:121 , ASP D:123 , ASP D:132 , HIS D:137 , SER D:147
BINDING SITE FOR RESIDUE MN D 4238
09
AC9
SOFTWARE
ASP E:123 , TYR E:125 , ASN E:127 , ASP E:132
BINDING SITE FOR RESIDUE CA E 5237
10
BC1
SOFTWARE
GLU E:121 , ASP E:123 , ASP E:132 , HIS E:137 , VAL E:145 , SER E:147
BINDING SITE FOR RESIDUE MN E 5238
11
BC2
SOFTWARE
GLY F:104 , ASP F:123 , TYR F:125 , ASN F:127 , ASP F:132
BINDING SITE FOR RESIDUE CA F 6237
12
BC3
SOFTWARE
GLU F:121 , ASP F:123 , ASP F:132 , HIS F:137
BINDING SITE FOR RESIDUE MN F 6238
13
BC4
SOFTWARE
ASP G:123 , TYR G:125 , ASN G:127 , ASP G:132
BINDING SITE FOR RESIDUE CA G 7237
14
BC5
SOFTWARE
GLU G:121 , ASP G:123 , ASP G:132 , HIS G:137 , VAL G:145
BINDING SITE FOR RESIDUE MN G 7238
15
BC6
SOFTWARE
GLY H:104 , ASP H:123 , TYR H:125 , ASN H:127 , ASP H:132
BINDING SITE FOR RESIDUE CA H 8237
16
BC7
SOFTWARE
GLU H:121 , ASP H:123 , ASP H:132 , HIS H:137
BINDING SITE FOR RESIDUE MN H 8238
[
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]
SAPs(SNPs)/Variants
(3, 24)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_LECG_ARAHY_001 (E92V, chain A/B/C/D/E/F/G/H, )
2: VAR_LECG_ARAHY_002 (K149A, chain A/B/C/D/E/F/G/H, )
3: VAR_LECG_ARAHY_003 (K162I, chain A/B/C/D/E/F/G/H, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_LECG_ARAHY_001
*
E
115
V
LECG_ARAHY
---
---
A/B/C/D/E/F/G/H
E
92
V
2
UniProt
VAR_LECG_ARAHY_002
*
K
172
A
LECG_ARAHY
---
---
A/B/C/D/E/F/G/H
K
149
A
3
UniProt
VAR_LECG_ARAHY_003
*
K
185
I
LECG_ARAHY
---
---
A/B/C/D/E/F/G/H
K
162
I
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(2, 16)
Info
All PROSITE Patterns/Profiles
1: LECTIN_LEGUME_BETA (A:118-124,B:118-124,C:118-124,D:11...)
2: LECTIN_LEGUME_ALPHA (A:198-207,B:198-207,C:198-207,D:19...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LECTIN_LEGUME_BETA
PS00307
Legume lectins beta-chain signature.
LECG_ARAHY
141-147
8
A:118-124
B:118-124
C:118-124
D:118-124
E:118-124
F:118-124
G:118-124
H:118-124
2
LECTIN_LEGUME_ALPHA
PS00308
Legume lectins alpha-chain signature.
LECG_ARAHY
221-230
8
A:198-207
B:198-207
C:198-207
D:198-207
E:198-207
F:198-207
G:198-207
H:198-207
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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
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1v6na_ (A:)
1b: SCOP_d1v6nb_ (B:)
1c: SCOP_d1v6nc_ (C:)
1d: SCOP_d1v6nd_ (D:)
1e: SCOP_d1v6ne_ (E:)
1f: SCOP_d1v6nf_ (F:)
1g: SCOP_d1v6ng_ (G:)
1h: SCOP_d1v6nh_ (H:)
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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)
Peanut (Arachis hypogaea) [TaxId: 3818]
(23)
1a
d1v6na_
A:
1b
d1v6nb_
B:
1c
d1v6nc_
C:
1d
d1v6nd_
D:
1e
d1v6ne_
E:
1f
d1v6nf_
F:
1g
d1v6ng_
G:
1h
d1v6nh_
H:
[
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1v6nA00 (A:1-232)
1b: CATH_1v6nE00 (E:1-232)
1c: CATH_1v6nF00 (F:1-232)
1d: CATH_1v6nG00 (G:1-232)
1e: CATH_1v6nH00 (H:1-232)
1f: CATH_1v6nB00 (B:1-232)
1g: CATH_1v6nC00 (C:1-232)
1h: CATH_1v6nD00 (D:1-232)
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)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.200, no name defined]
(421)
Peanut (Arachis hypogaea)
(22)
1a
1v6nA00
A:1-232
1b
1v6nE00
E:1-232
1c
1v6nF00
F:1-232
1d
1v6nG00
G:1-232
1e
1v6nH00
H:1-232
1f
1v6nB00
B:1-232
1g
1v6nC00
C:1-232
1h
1v6nD00
D:1-232
[
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Lectin_legB_1v6nH01 (H:2-226)
1b: PFAM_Lectin_legB_1v6nH02 (H:2-226)
1c: PFAM_Lectin_legB_1v6nH03 (H:2-226)
1d: PFAM_Lectin_legB_1v6nH04 (H:2-226)
1e: PFAM_Lectin_legB_1v6nH05 (H:2-226)
1f: PFAM_Lectin_legB_1v6nH06 (H:2-226)
1g: PFAM_Lectin_legB_1v6nH07 (H:2-226)
1h: PFAM_Lectin_legB_1v6nH08 (H:2-226)
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)
Clan
:
Concanavalin
(293)
Family
:
Lectin_legB
(93)
Arachis hypogaea (Peanut)
(11)
1a
Lectin_legB-1v6nH01
H:2-226
1b
Lectin_legB-1v6nH02
H:2-226
1c
Lectin_legB-1v6nH03
H:2-226
1d
Lectin_legB-1v6nH04
H:2-226
1e
Lectin_legB-1v6nH05
H:2-226
1f
Lectin_legB-1v6nH06
H:2-226
1g
Lectin_legB-1v6nH07
H:2-226
1h
Lectin_legB-1v6nH08
H:2-226
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Asym.Unit (264 KB)
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