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1MDT
Asym. Unit
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Asym.Unit (174 KB)
Biol.Unit 1 (169 KB)
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(1)
Title
:
THE REFINED STRUCTURE OF MONOMERIC DIPHTHERIA TOXIN AT 2.3 ANGSTROMS RESOLUTION
Authors
:
M. J. Bennett, D. Eisenberg
Date
:
21 Mar 94 (Deposition) - 31 Jul 94 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Toxin
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
M. J. Bennett, D. Eisenberg
Refined Structure Of Monomeric Diphtheria Toxin At 2. 3 A Resolution.
Protein Sci. V. 3 1464 1994
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: ADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-... (APUa)
1b: ADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-... (APUb)
View:
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No.
Name
Count
Type
Full Name
1
APU
2
Ligand/Ion
ADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-MONOPHOSPHATE
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: CAT (AUTHOR)
4: CBT (AUTHOR)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:21 , GLY A:22 , LYS A:24 , GLY A:34 , ILE A:35 , GLN A:36 , PRO A:38 , THR A:42 , GLY A:44 , PHE A:53 , TYR A:54 , TYR A:65 , TRP A:153 , SER A:446 , ARG A:458 , HOH A:538 , HOH A:539 , HOH A:586 , HOH A:588 , HOH A:590 , HOH A:667
BINDING SITE FOR RESIDUE APU A 901
2
AC2
SOFTWARE
HIS B:21 , GLY B:22 , LYS B:24 , TYR B:27 , ILE B:31 , GLY B:34 , ILE B:35 , GLN B:36 , THR B:42 , GLY B:44 , ASN B:45 , TYR B:54 , TYR B:65 , TRP B:153 , SER B:446 , ARG B:458 , HOH B:906 , HOH B:951 , HOH B:953 , HOH B:955 , HOH B:975 , HOH B:1003 , HOH B:1075
BINDING SITE FOR RESIDUE APU B 901
3
CAT
AUTHOR
HIS A:21 , TYR A:65 , GLU A:148 , SER A:446 , ARG A:458
CATALYTIC SITE IN CHAIN A
4
CBT
AUTHOR
HIS B:21 , TYR B:65 , GLU B:148 , SER B:446 , ARG B:458
CATALYTIC SITE IN CHAIN B
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1mdta1 (A:381-535)
1b: SCOP_d1mdtb1 (B:381-535)
2a: SCOP_d1mdta2 (A:1-187)
2b: SCOP_d1mdtb2 (B:1-187)
3a: SCOP_d1mdta3 (A:200-380)
3b: SCOP_d1mdtb3 (B:200-380)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Common fold of diphtheria toxin/transcription factors/cytochrome f
(364)
Superfamily
:
Diphtheria toxin, C-terminal domain
(9)
Family
:
Diphtheria toxin, C-terminal domain
(7)
Protein domain
:
Diphtheria toxin, C-terminal domain
(7)
Corynebacterium diphtheriae [TaxId: 1717]
(7)
1a
d1mdta1
A:381-535
1b
d1mdtb1
B:381-535
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ADP-ribosylation
(157)
Superfamily
:
ADP-ribosylation
(157)
Family
:
ADP-ribosylating toxins
(85)
Protein domain
:
Diphtheria toxin, N-terminal domain
(8)
Corynebacterium diphtheriae [TaxId: 1717]
(8)
2a
d1mdta2
A:1-187
2b
d1mdtb2
B:1-187
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Toxins' membrane translocation domains
(135)
Superfamily
:
Diphtheria toxin, middle domain
(9)
Family
:
Diphtheria toxin, middle domain
(7)
Protein domain
:
Diphtheria toxin, middle domain
(7)
Corynebacterium diphtheriae [TaxId: 1717]
(7)
3a
d1mdta3
A:200-380
3b
d1mdtb3
B:200-380
[
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1mdtA01 (A:1-187)
1b: CATH_1mdtB01 (B:1-187)
2a: CATH_1mdtA02 (A:200-379)
2b: CATH_1mdtB02 (B:200-379)
3a: CATH_1mdtA03 (A:380-534)
3b: CATH_1mdtB03 (B:380-534)
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)
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)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Diphtheria Toxin; domain 1
(22)
Homologous Superfamily
:
Diphtheria Toxin, domain 1
(22)
Corynephage beta. Organism_taxid: 10703
(3)
1a
1mdtA01
A:1-187
1b
1mdtB01
B:1-187
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Globin-like
(786)
Homologous Superfamily
:
Diphtheria toxin, middle domain
(6)
Corynephage beta. Organism_taxid: 10703
(2)
2a
1mdtA02
A:200-379
2b
1mdtB02
B:200-379
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.700, no name defined]
(6)
Corynephage beta. Organism_taxid: 10703
(2)
3a
1mdtA03
A:380-534
3b
1mdtB03
B:380-534
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Diphtheria_C_1mdtB01 (B:1-187)
1b: PFAM_Diphtheria_C_1mdtB02 (B:1-187)
2a: PFAM_Diphtheria_R_1mdtB03 (B:381-534)
2b: PFAM_Diphtheria_R_1mdtB04 (B:381-534)
3a: PFAM_Diphtheria_T_1mdtB05 (B:200-379)
3b: PFAM_Diphtheria_T_1mdtB06 (B:200-379)
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Clans
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(
)
Organisms
(
)
(
)
Clan
:
ADP-ribosyl
(56)
Family
:
Diphtheria_C
(4)
Corynephage beta
(4)
1a
Diphtheria_C-1mdtB01
B:1-187
1b
Diphtheria_C-1mdtB02
B:1-187
Clan
:
no clan defined [family: Diphtheria_R]
(4)
Family
:
Diphtheria_R
(4)
Corynephage beta
(4)
2a
Diphtheria_R-1mdtB03
B:381-534
2b
Diphtheria_R-1mdtB04
B:381-534
Clan
:
no clan defined [family: Diphtheria_T]
(4)
Family
:
Diphtheria_T
(4)
Corynephage beta
(4)
3a
Diphtheria_T-1mdtB05
B:200-379
3b
Diphtheria_T-1mdtB06
B:200-379
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