SMTL ID : 5x5x.1

Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

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

PEG.1: 5 residues within 4Å: Chain A: K.42, K.67, K.71, E.93, D.94 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.42, A:K.42 Water bridges: A:K.67 PEG.2: 6 residues within 4Å: Chain A: Y.99, Q.112, T.115 Chain B: Q.45, G.48, Q.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.115, A:T.115 Water bridges: A:T.115 PEG.3: 3 residues within 4Å: Chain A: D.59, G.60, Y.61 No protein-ligand interaction detected (PLIP) PEG.4: 6 residues within 4Å: Chain A: N.34, N.35, Y.36, W.37, D.56, S.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.34, A:Y.36, A:W.37

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 12 residues within 4Å: Chain A: H.39, V.41, T.101, S.103, T.104, G.107 Chain B: Y.39, H.41, Y.43, T.57, T.98 Ligands: PGE.10 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.43 Water bridges: B:T.57, A:T.104 PG4.6: 4 residues within 4Å: Chain A: K.23, T.75, Y.84, H.86 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.23

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.7: 3 residues within 4Å: Chain A: Q.9, S.25, K.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.9, A:S.25 FMT.8: 5 residues within 4Å: Chain A: T.28, S.29, G.30, Y.36, S.81 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.30, A:Y.36, A:Y.36, A:S.81 FMT.11: 2 residues within 4Å: Chain B: L.17, S.175 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.175 Water bridges: B:S.178

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 4 residues within 4Å: Chain B: L.11, I.92, G.107, K.110 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.149 PGE.10: 6 residues within 4Å: Chain A: W.37, E.54, S.103 Chain B: H.33, Y.103 Ligands: PG4.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.33, B:Y.103, B:Y.103, A:S.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arai, R. et al., Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219. To be published

Release Date

2018-02-21

Peptides

Fd chain of anti-osteocalcin antibody KTM219: A
L chain of anti-osteocalcin antibody KTM219: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

Fd chain of anti-osteocalcin antibody KTM219

L chain of anti-osteocalcin antibody KTM219