SMTL ID : 3iet.1 (2 other biounits)

Crystal Structure of 237mAb with antigen

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GLY- THR- LYS- PRO- PRO- LEU- GLU- GLU- LEU: Podoplanin(Non-covalent)

GLY-THR-LYS-PRO-PRO-LEU-GLU-GLU-LEU.1: 14 residues within 4Å: Chain A: H.31, N.33, N.35, Y.37, K.55, T.97, H.98, V.99 Chain B: W.33, R.52, N.53, A.55, N.56 Ligands: A2G.7 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:N.33, A:N.35, A:T.97, B:R.52, B:R.52, B:N.53, B:N.56, B:N.56 Water bridges: A:H.31 Salt bridges: A:K.55 Hydrophobic interactions: B:W.33 GLY-THR-LYS-PRO-PRO-LEU-GLU-GLU-LEU.2: 9 residues within 4Å: Chain C: H.31, N.33, T.97, H.98 Chain D: W.33, R.52, N.56, Y.61 Ligands: A2G.8 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.33 Hydrogen bonds: D:R.52, D:R.52, D:N.56, D:N.56, C:T.97

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: R.159, E.189, H.193 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.189, A:E.189, A:H.193, H2O.3, H2O.4 ZN.4: 1 residues within 4Å: Chain B: H.58 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.58, H2O.9 ZN.5: 1 residues within 4Å: Chain C: E.127 No protein-ligand interaction detected (PLIP) ZN.6: 2 residues within 4Å: Chain A: D.147 Chain D: H.58 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:D.147, A:D.147, D:H.58, H2O.5

2 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.7: 15 residues within 4Å: Chain A: H.31, Y.37, S.96, T.97, H.98 Chain B: W.33, W.47, E.50, R.52, Y.61, R.104 Ligands: GLY-THR-LYS-PRO-PRO-LEU-GLU-GLU-LEU.1, GLY-THR-LYS-PRO-PRO-LEU-GLU-GLU-LEU.1, GLY-THR-LYS-PRO-PRO-LEU-GLU-GLU-LEU.1, GLY-THR-LYS-PRO-PRO-LEU-GLU-GLU-LEU.1 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.52, B:R.104, A:S.96, A:T.97 Hydrophobic interactions: A:Y.37 Water bridges: A:S.96 A2G.8: 16 residues within 4Å: Chain C: H.31, Y.37, S.96, T.97, H.98, P.100 Chain D: W.33, W.47, E.50, R.52, Y.61, R.104 Ligands: GLY-THR-LYS-PRO-PRO-LEU.2, GLY-THR-LYS-PRO-PRO-LEU.2, GLY-THR-LYS-PRO-PRO-LEU.2, GLY-THR-LYS-PRO-PRO-LEU.2 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:R.52, D:R.104, C:S.96, C:T.97 Hydrophobic interactions: C:Y.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brooks, C.L. et al., Antibody recognition of a unique tumor-specific glycopeptide antigen. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-06-23

Peptides

Immunoglobulin light chain (IgG2a): AC
Immunoglobulin heavy chain (IgG2a): BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Immunoglobulin light chain (IgG2a)

Immunoglobulin heavy chain (IgG2a)

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