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2RKM
Asym. Unit
Info
Asym.Unit (101 KB)
Biol.Unit 1 (96 KB)
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(1)
Title
:
STRUCTURE OF OPPA COMPLEXED WITH LYS-LYS
Authors
:
S. H. Sleigh, J. R. H. Tame, A. J. Wilkinson
Date
:
25 Mar 97 (Deposition) - 29 Jul 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Peptide Transport, Complex (Binding Protein/Dipeptide), Peptide Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. H. Sleigh, J. R. Tame, E. J. Dodson, A. J. Wilkinson
Peptide Binding In Oppa, The Crystal Structures Of The Periplasmic Oligopeptide Binding Protein In The Unliganded Form And In Complex With Lysyllysine.
Biochemistry V. 36 9747 1997
(for further references see the
PDB file header
)
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Hetero Components
(2, 10)
Info
All Hetero Components
1a: URANYL (VI) ION (IUMa)
1b: URANYL (VI) ION (IUMb)
1c: URANYL (VI) ION (IUMc)
1d: URANYL (VI) ION (IUMd)
1e: URANYL (VI) ION (IUMe)
1f: URANYL (VI) ION (IUMf)
1g: URANYL (VI) ION (IUMg)
1h: URANYL (VI) ION (IUMh)
2a: LYSINE (LYSa)
2b: LYSINE (LYSb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IUM
8
Ligand/Ion
URANYL (VI) ION
2
LYS
2
Mod. Amino Acid
LYSINE
[
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]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:32 , SER A:37 , TYR A:109 , TRP A:416 , CYS A:417 , ALA A:418 , ASP A:419 , LYS A:2002 , HOH A:2520
BINDING SITE FOR RESIDUE LYS A 2001
02
AC2
SOFTWARE
GLU A:32 , GLY A:33 , VAL A:34 , TRP A:397 , GLY A:415 , TRP A:416 , ASN A:436 , THR A:438 , LYS A:2001 , HOH A:2025 , HOH A:2517 , HOH A:2518 , HOH A:2519 , HOH A:2521
BINDING SITE FOR RESIDUE LYS A 2002
03
AC3
SOFTWARE
ASP A:323 , GLU A:393 , ASN A:394 , HOH A:2026 , HOH A:2049 , HOH A:2141 , HOH A:2241
BINDING SITE FOR RESIDUE IUM A 518
04
AC4
SOFTWARE
LYS A:372 , IUM A:520 , HOH A:2032 , HOH A:2065 , HOH A:2080 , HOH A:2099 , HOH A:2124 , HOH A:2171 , HOH A:2371
BINDING SITE FOR RESIDUE IUM A 519
05
AC5
SOFTWARE
PRO A:153 , LYS A:372 , ASP A:459 , IUM A:519 , HOH A:2064 , HOH A:2080 , HOH A:2093 , HOH A:2097 , HOH A:2154
BINDING SITE FOR RESIDUE IUM A 520
06
AC6
SOFTWARE
VAL A:230 , GLU A:251 , ASP A:369 , LYS A:373 , HOH A:2047 , HOH A:2111 , HOH A:2295
BINDING SITE FOR RESIDUE IUM A 521
07
AC7
SOFTWARE
GLU A:53 , LYS A:281 , ASP A:362 , ASP A:410 , HOH A:2142
BINDING SITE FOR RESIDUE IUM A 522
08
AC8
SOFTWARE
PRO A:130 , ASP A:133 , HIS A:517 , IUM A:524 , HOH A:2462
BINDING SITE FOR RESIDUE IUM A 523
09
AC9
SOFTWARE
IUM A:523 , IUM A:525 , HOH A:2143 , HOH A:2277 , HOH A:2293 , HOH A:2462
BINDING SITE FOR RESIDUE IUM A 524
10
BC1
SOFTWARE
ASP A:11 , GLU A:342 , IUM A:524 , HOH A:2145 , HOH A:2213 , HOH A:2470
BINDING SITE FOR RESIDUE IUM A 525
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: SBP_BACTERIAL_5 (A:61-82)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SBP_BACTERIAL_5
PS01040
Bacterial extracellular solute-binding proteins, family 5 signature.
OPPA_SALTY
87-108
1
A:61-82
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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, 1)
Info
All SCOP Domains
1a: SCOP_d2rkma_ (A:)
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(
)
(
)
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)
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)
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Periplasmic binding protein-like II
(813)
Superfamily
:
Periplasmic binding protein-like II
(813)
Family
:
Phosphate binding protein-like
(463)
Protein domain
:
Oligo-peptide binding protein (OPPA)
(34)
Salmonella typhimurium [TaxId: 90371]
(32)
1a
d2rkma_
A:
[
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2rkmA01 (A:1-44,A:169-270,A:487-517)
2a: CATH_2rkmA02 (A:45-168)
3a: CATH_2rkmA03 (A:271-486)
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)
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)
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)
(
)
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)
Salmonella typhimurium. Organism_taxid: 602.
(24)
1a
2rkmA01
A:1-44,A:169-270,A:487-517
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Dipeptide-binding Protein; domain 1
(35)
Homologous Superfamily
:
Dipeptide-binding Protein; Domain 1
(35)
Salmonella typhimurium. Organism_taxid: 602.
(24)
2a
2rkmA02
A:45-168
Architecture
:
Roll
(3276)
Topology
:
Dipeptide-binding Protein; domain 3
(35)
Homologous Superfamily
:
Dipeptide-binding Protein; Domain 3
(35)
Salmonella typhimurium. Organism_taxid: 602.
(24)
3a
2rkmA03
A:271-486
[
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_SBP_bac_5_2rkmA01 (A:55-438)
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)
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)
(
)
Clan
:
PBP
(391)
Family
:
SBP_bac_5
(33)
Salmonella typhimurium
(9)
1a
SBP_bac_5-2rkmA01
A:55-438
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Chain A
Asymmetric Unit 1
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Asym.Unit (101 KB)
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