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1RIT
Asym. Unit
Info
Asym.Unit (171 KB)
Biol.Unit 1 (160 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PEANUT LECTIN IN COMPLEX WITH MESO-TETRASULPHONATOPHENYLPORPHYRIN AND LACTOSE
Authors
:
M. Goel, K. J. Kaur, B. G. Maiya, M. J. Swamy, D. M. Salunke
Date
:
17 Nov 03 (Deposition) - 28 Dec 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.85
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Sugar Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Goel, R. S. Damai, D. K. Sethi, K. J. Kaur, B. G. Maiya, M. J. Swamy, D. M. Salunke
Crystal Structures Of The Pna-Porphyrin Complex In The Presence And Absence Of Lactose: Mapping The Conformational Changes On Lactose Binding, Interacting Surfaces, And Supramolecular Aggregations.
Biochemistry V. 44 5588 2005
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 21)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: BETA-LACTOSE (LATa)
2b: BETA-LACTOSE (LATb)
3a: MANGANESE (II) ION (MNa)
3b: MANGANESE (II) ION (MNb)
3c: MANGANESE (II) ION (MNc)
3d: MANGANESE (II) ION (MNd)
4a: 5,10,15,20-TETRAKIS(4-SULPFONATOPH... (SFPa)
4b: 5,10,15,20-TETRAKIS(4-SULPFONATOPH... (SFPb)
4c: 5,10,15,20-TETRAKIS(4-SULPFONATOPH... (SFPc)
4d: 5,10,15,20-TETRAKIS(4-SULPFONATOPH... (SFPd)
4e: 5,10,15,20-TETRAKIS(4-SULPFONATOPH... (SFPe)
4f: 5,10,15,20-TETRAKIS(4-SULPFONATOPH... (SFPf)
4g: 5,10,15,20-TETRAKIS(4-SULPFONATOPH... (SFPg)
4h: 5,10,15,20-TETRAKIS(4-SULPFONATOPH... (SFPh)
4i: 5,10,15,20-TETRAKIS(4-SULPFONATOPH... (SFPi)
4j: 5,10,15,20-TETRAKIS(4-SULPFONATOPH... (SFPj)
4k: 5,10,15,20-TETRAKIS(4-SULPFONATOPH... (SFPk)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
LAT
2
Ligand/Ion
BETA-LACTOSE
3
MN
4
Ligand/Ion
MANGANESE (II) ION
4
SFP
11
Ligand/Ion
5,10,15,20-TETRAKIS(4-SULPFONATOPHENYL)-21H,23H-PORPHINE
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP C:80 , ASP C:83 , GLY C:104 , TYR C:125 , ASN C:127 , SER C:211 , LEU C:212 , GLY C:213 , GLY C:214 , HOH C:261
BINDING SITE FOR RESIDUE LAT C 246
02
AC2
SOFTWARE
ASP D:80 , ASP D:83 , GLY D:103 , GLY D:104 , TYR D:125 , ASN D:127 , SER D:211 , LEU D:212 , GLY D:213
BINDING SITE FOR RESIDUE LAT D 247
03
AC3
SOFTWARE
ASP A:123 , TYR A:125 , ASN A:127 , ASP A:132
BINDING SITE FOR RESIDUE CA A 248
04
AC4
SOFTWARE
GLU A:121 , ASP A:123 , ASP A:132 , HIS A:137
BINDING SITE FOR RESIDUE MN A 249
05
AC5
SOFTWARE
ASP B:123 , TYR B:125 , ASN B:127 , ASP B:132
BINDING SITE FOR RESIDUE CA B 250
06
AC6
SOFTWARE
GLU B:121 , ASP B:123 , ASP B:132 , HIS B:137
BINDING SITE FOR RESIDUE MN B 251
07
AC7
SOFTWARE
ASP C:123 , TYR C:125 , ASN C:127 , ASP C:132
BINDING SITE FOR RESIDUE CA C 252
08
AC8
SOFTWARE
GLU C:121 , ASP C:123 , ASP C:132 , HIS C:137 , SER C:147 , HOH C:256
BINDING SITE FOR RESIDUE MN C 253
09
AC9
SOFTWARE
ASP D:123 , TYR D:125 , ASN D:127 , ASP D:132
BINDING SITE FOR RESIDUE CA D 254
10
BC1
SOFTWARE
GLU D:121 , ASP D:123 , ASP D:132 , HIS D:137 , VAL D:145 , SER D:147
BINDING SITE FOR RESIDUE MN D 255
11
BC2
SOFTWARE
ARG A:215 , SFP A:243 , SFP A:251 , PRO D:134 , THR D:135
BINDING SITE FOR RESIDUE SFP A 250
12
BC3
SOFTWARE
ASN A:41 , SER A:100 , ILE A:101 , LEU A:212 , SFP A:250 , SFP C:240 , PRO D:134
BINDING SITE FOR RESIDUE SFP A 251
13
BC4
SOFTWARE
ASN B:38 , ARG B:215 , SFP B:238 , THR C:135
BINDING SITE FOR RESIDUE SFP B 237
14
BC5
SOFTWARE
ASN B:41 , ILE B:101 , LEU B:212 , SFP B:237 , PRO C:134 , SFP D:242
BINDING SITE FOR RESIDUE SFP B 238
15
BC6
SOFTWARE
ARG C:53 , SER C:56 , THR C:59 , THR C:231 , SFP C:240
BINDING SITE FOR RESIDUE SFP C 239
16
BC7
SOFTWARE
THR A:111 , LEU A:212 , SFP A:251 , ARG C:53 , ALA C:58 , SFP C:239 , HOH C:254
BINDING SITE FOR RESIDUE SFP C 240
17
BC8
SOFTWARE
ARG D:53 , SER D:56 , THR D:231 , SFP D:242 , HOH D:257
BINDING SITE FOR RESIDUE SFP D 241
18
BC9
SOFTWARE
THR B:111 , SFP B:238 , ARG D:53 , ALA D:58 , SFP D:241
BINDING SITE FOR RESIDUE SFP D 242
19
CC1
SOFTWARE
THR A:25 , LEU A:27 , ASN A:29 , ASN A:31 , GLN A:33 , LEU A:37 , ASN A:38 , GLU A:72 , ASP A:75 , TYR A:79 , ILE A:217 , LEU A:219 , ARG A:221 , SFP A:244 , SFP A:250 , HOH A:263
BINDING SITE FOR RESIDUE SFP A 243
20
CC2
SOFTWARE
SER A:28 , ASN A:29 , SFP A:243 , SER B:28 , ASN B:29 , LYS B:74 , SFP B:245
BINDING SITE FOR RESIDUE SFP A 244
21
CC3
SOFTWARE
SFP A:244 , THR B:25 , ASN B:29 , ASN B:31 , GLN B:33 , ASN B:38 , GLU B:72 , ASP B:75 , ILE B:217 , LEU B:219
BINDING SITE FOR RESIDUE SFP B 245
[
close Site info
]
SAPs(SNPs)/Variants
(3, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_LECG_ARAHY_001 (E92V, chain A/B/C/D, )
2: VAR_LECG_ARAHY_002 (K149A, chain A/B/C/D, )
3: VAR_LECG_ARAHY_003 (K162I, chain A/B/C/D, )
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
92
V
2
UniProt
VAR_LECG_ARAHY_002
*
K
172
A
LECG_ARAHY
---
---
A/B/C/D
K
149
A
3
UniProt
VAR_LECG_ARAHY_003
*
K
185
I
LECG_ARAHY
---
---
A/B/C/D
K
162
I
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
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
4
A:118-124
B:118-124
C:118-124
D:118-124
2
LECTIN_LEGUME_ALPHA
PS00308
Legume lectins alpha-chain signature.
LECG_ARAHY
221-230
4
A:198-207
B:198-207
C:198-207
D:198-207
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1rita_ (A:)
1b: SCOP_d1ritb_ (B:)
1c: SCOP_d1ritc_ (C:)
1d: SCOP_d1ritd_ (D:)
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Protein Domains
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)
(
)
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
d1rita_
A:
1b
d1ritb_
B:
1c
d1ritc_
C:
1d
d1ritd_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1ritA00 (A:1-232)
1b: CATH_1ritB00 (B:1-232)
1c: CATH_1ritC00 (C:1-232)
1d: CATH_1ritD00 (D:1-232)
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Homologous Superfamilies
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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
1ritA00
A:1-232
1b
1ritB00
B:1-232
1c
1ritC00
C:1-232
1d
1ritD00
D:1-232
[
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]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Lectin_legB_1ritD01 (D:2-226)
1b: PFAM_Lectin_legB_1ritD02 (D:2-226)
1c: PFAM_Lectin_legB_1ritD03 (D:2-226)
1d: PFAM_Lectin_legB_1ritD04 (D:2-226)
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Clans
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)
Organisms
(
)
(
)
Clan
:
Concanavalin
(293)
Family
:
Lectin_legB
(93)
Arachis hypogaea (Peanut)
(11)
1a
Lectin_legB-1ritD01
D:2-226
1b
Lectin_legB-1ritD02
D:2-226
1c
Lectin_legB-1ritD03
D:2-226
1d
Lectin_legB-1ritD04
D:2-226
[
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Asym.Unit (171 KB)
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