SMTL ID : 1p7k.1 (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

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

SO4.1: 2 residues within 4Å: Chain A: R.108, D.170 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.108 Salt bridges: A:R.108 SO4.10: 4 residues within 4Å: Chain B: V.2, Y.27, Y.32, R.98 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.32 Water bridges: B:R.98, B:R.98 Salt bridges: B:R.98 SO4.11: 4 residues within 4Å: Chain B: Y.27, T.28, S.31, Y.32 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:S.31 SO4.12: 5 residues within 4Å: Chain A: G.93, T.94 Chain B: K.59, Y.105 Ligands: EPE.2 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.105, B:Y.105, A:T.94 Water bridges: B:Y.104, A:T.94, A:T.94 Salt bridges: B:K.59 SO4.13: 1 residues within 4Å: Chain B: Y.101 No protein-ligand interaction detected (PLIP) SO4.14: 4 residues within 4Å: Chain B: S.165, L.166, S.167, S.168 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.165, B:S.167, B:S.168 Water bridges: B:G.169, B:G.169

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

EPE.2: 9 residues within 4Å: Chain A: Y.32, H.91, Y.92 Chain B: R.102, P.103, Y.104, Y.105, A.106 Ligands: SO4.12 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.3: 10 residues within 4Å: Chain A: S.31, A.51, K.52, G.64, S.65, G.66, S.67, Q.70, F.71, S.72 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.31, A:G.66 Water bridges: A:S.67, A:S.67 1PE.15: 7 residues within 4Å: Chain B: V.33, Y.50, N.52, Y.54, N.55, Y.104 Ligands: PEG.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.52, B:N.55, B:N.55

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: I.150, D.151, S.153, R.155, H.189 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.155 PEG.16: 3 residues within 4Å: Chain B: S.31, Y.101 Ligands: 1PE.15 No protein-ligand interaction detected (PLIP)

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: S.31, Y.32, N.50 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.31, A:S.31, A:N.50 GOL.6: 3 residues within 4Å: Chain A: P.8, A.9, S.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.9, A:S.10 GOL.7: 8 residues within 4Å: Chain A: P.119, F.209, N.210, R.211, E.213 Chain B: G.134, S.135, R.220 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.135, A:N.210, A:R.211 Water bridges: B:A.136, A:N.210 GOL.8: 6 residues within 4Å: Chain A: Q.38, K.39, Q.40, G.41, K.42 Chain B: Y.95 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.39, A:G.41, A:K.42 Water bridges: B:Q.112, B:Q.112 GOL.9: 6 residues within 4Å: Chain A: Q.37, Q.45, L.47, E.56, G.57, P.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.45 GOL.17: 5 residues within 4Å: Chain B: K.38, E.46, K.63, F.64, E.89 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.38, B:E.46, B:D.90 GOL.18: 7 residues within 4Å: Chain B: K.38, Q.39, K.40, Q.43, G.44, L.45, E.46 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.40, B:K.40, B:E.46 Water bridges: B:L.45 GOL.19: 9 residues within 4Å: Chain A: S.162, S.176, T.178 Chain B: F.173, P.174, V.176, T.183, L.184, S.185 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:P.174, B:S.185, A:S.162, A:S.176, A:T.178

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
L

B
H

antibody light chain FAB

antibody heavy chain FAB

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