SMTL ID : 4nja.1

Crystal structure of Fab 6C8 in complex with MPTS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: E.27, E.97 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.27, A:E.27, A:E.97, A:E.97 ZN.6: 3 residues within 4Å: Chain A: N.142, D.171 Chain B: H.172 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.172, H2O.2

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: Q.41, K.43, P.63, F.66, D.86 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.63, A:F.66 Hydrogen bonds: A:Q.41, A:D.86 Salt bridges: A:K.43 ACT.3: 1 residues within 4Å: Chain A: K.146 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.146

1 x 2M9: 8-methoxypyrene-1,3,6-trisulfonic acid(Non-covalent)

2M9.4: 10 residues within 4Å: Chain A: Y.32, N.34, F.36, R.54 Chain B: G.101, Y.102, G.103, I.104, R.105, G.106 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Y.102, B:G.103, B:R.105, A:N.34 Water bridges: B:Y.107, B:Y.107 Salt bridges: B:R.105, A:R.54 Hydrophobic interactions: A:Y.32, A:Y.32 pi-Stacking: A:F.36

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

PO4.5: 3 residues within 4Å: Chain A: E.59 Chain B: Y.107, D.109 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.107, B:D.109, A:E.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adhikary, R. et al., Adaptive Mutations Alter Antibody Structure and Dynamics during Affinity Maturation. Biochemistry (2015)

Release Date

2014-11-12

Peptides

6C8 light chain: A
6C8 heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

6C8 light chain

6C8 heavy chain