SMTL ID : 2oje.3 (2 other biounits)

Mycoplasma arthritidis-derived mitogen complexed with class II MHC molecule HLA-DR1/HA complex in the presence of EDTA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-4-4-4-4-mer

Ligands

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: E.54, G.57 Chain C: K.2, K.5 Chain D: K.11, K.114 Ligands: PO4.2 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Salt bridges: C:K.2, C:K.5, D:K.114 PO4.2: 8 residues within 4Å: Chain A: A.60 Chain C: K.5 Chain D: A.12, Q.13, H.15, K.114, D.118 Ligands: PO4.1 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.13, D:Q.13, D:K.83 Salt bridges: D:H.15, D:K.114, C:K.5 PO4.3: 7 residues within 4Å: Chain E: E.54, G.57 Chain G: K.2, K.5 Chain H: K.11, K.114 Ligands: PO4.4 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H Salt bridges: G:K.2, G:K.5, H:K.114 PO4.4: 8 residues within 4Å: Chain E: A.60 Chain G: K.5 Chain H: A.12, Q.13, H.15, K.114, D.118 Ligands: PO4.3 6 PLIP interactions: 1 interactions with chain G, 5 interactions with chain H Salt bridges: G:K.5, H:H.15, H:K.114 Hydrogen bonds: H:Q.13, H:Q.13, H:K.83 PO4.5: 5 residues within 4Å: Chain I: E.54, G.57 Chain K: K.5 Chain L: K.114 Ligands: PO4.6 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain L Salt bridges: K:K.5, L:K.114 PO4.6: 8 residues within 4Å: Chain I: A.60 Chain K: K.5 Chain L: A.12, Q.13, H.15, K.114, D.118 Ligands: PO4.5 6 PLIP interactions: 1 interactions with chain K, 5 interactions with chain L Salt bridges: K:K.5, L:H.15, L:K.114 Hydrogen bonds: L:Q.13, L:Q.13, L:D.118 PO4.7: 5 residues within 4Å: Chain M: E.54, G.57 Chain O: K.5 Chain P: K.114 Ligands: PO4.8 2 PLIP interactions: 1 interactions with chain O, 1 interactions with chain P Salt bridges: O:K.5, P:K.114 PO4.8: 8 residues within 4Å: Chain M: A.60 Chain O: K.5 Chain P: A.12, Q.13, H.15, K.114, D.118 Ligands: PO4.7 6 PLIP interactions: 5 interactions with chain P, 1 interactions with chain O Hydrogen bonds: P:Q.13, P:Q.13, P:D.118 Salt bridges: P:H.15, P:K.114, O:K.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H. et al., Zinc induces dimerization of the class II major histocompatibility complex molecule that leads to cooperative binding to a superantigen. J.Biol.Chem. (2007)

Release Date

2007-01-23

Peptides

HLA class II histocompatibility antigen, DR alpha chain precursor: AEIM
HLA class II histocompatibility antigen, DRB1-1 beta chain precursor: BFJN
haemagglutinin peptide 306-318: CGKO
Superantigen: DHLP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
E

M
E

B
B

F
B

J
F

N
F

C
C

G
C

K
G

O
G

D
D

H
D

L
H

P
H

HLA class II histocompatibility antigen, DR alpha chain precursor

HLA class II histocompatibility antigen, DRB1-1 beta chain precursor

haemagglutinin peptide 306-318

Superantigen

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