SMTL ID : 1p7k.2 (1 other biounit)

Crystal structure of an anti-ssDNA antigen-binding fragment (Fab) bound to 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid (HEPES)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-mer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: K.142, W.163, T.164, D.165, Y.173 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.165 Water bridges: A:T.164 Salt bridges: A:K.142 SO4.6: 5 residues within 4Å: Chain A: G.93, T.94 Chain B: K.59, Y.105 Ligands: EPE.8 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.105, B:Y.105, A:T.94, A:T.94 Salt bridges: B:K.59 SO4.7: 3 residues within 4Å: Chain B: Y.27, T.28, Y.32 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:T.28

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: I.205, V.206, K.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.206, A:K.207 GOL.3: 3 residues within 4Å: Chain A: P.8, A.9, S.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.9, A:S.10, A:S.10 GOL.4: 7 residues within 4Å: Chain A: Q.124, S.127, G.128, G.129 Chain B: S.127, Y.129, K.150 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.127, B:S.127, A:Q.124, A:S.127 GOL.5: 5 residues within 4Å: Chain A: Q.40, F.83, Q.166, D.167, S.168 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.80, A:Q.166 Water bridges: A:D.167, A:S.168 GOL.11: 6 residues within 4Å: Chain B: K.38, E.46, K.63, F.64, E.89, D.90 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.38, B:K.38, B:D.90 GOL.12: 3 residues within 4Å: Chain B: Y.101, Y.104 Ligands: 1PE.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.101 GOL.13: 1 residues within 4Å: Chain B: K.74 No protein-ligand interaction detected (PLIP) GOL.14: 3 residues within 4Å: Chain A: S.127 Chain B: S.127, Y.129 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.127, B:Y.129, A:S.127, A:S.127 Water bridges: B:P.126, B:V.128

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.8: 8 residues within 4Å: Chain A: Y.32, H.91, Y.92, G.93 Chain B: P.103, Y.104, Y.105 Ligands: SO4.6 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.104, B:Y.105, B:A.106, A:H.91 Salt bridges: A:H.91

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.9: 9 residues within 4Å: Chain B: T.30, S.31, V.33, Y.50, N.52, Y.54, N.55, Y.104 Ligands: GOL.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.52, B:N.55 1PE.10: 9 residues within 4Å: Chain B: L.11, K.13, A.121, T.123, P.154, E.155, P.156, P.207, A.208 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.123 Water bridges: B:T.123, B:A.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schuermann, J.P. et al., Structure of an anti-DNA fab complexed with a non-DNA ligand provides insights into cross-reactivity and molecular mimicry. Proteins (2004)

Release Date

2004-05-11

Peptides

antibody light chain FAB: A
antibody heavy chain FAB: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

antibody light chain FAB

antibody heavy chain FAB

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