SMTL ID : 4nwt.1

Crystal structure of the anti-human NGF Fab APE1531

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-mer

Ligands

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 5 residues within 4Å: Chain A: C.220 Chain B: S.143, K.144, C.231 Ligands: MES.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.143 Water bridges: B:K.144 Salt bridges: B:K.144 MES.2: 5 residues within 4Å: Chain A: T.212, K.213, S.214 Chain B: K.144 Ligands: MES.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.214 Water bridges: A:K.213 Salt bridges: A:K.213, B:K.144

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

ACT.3: 8 residues within 4Å: Chain A: Q.43, K.45, K.51, P.65, R.67, F.68, E.87, D.88 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.65 Hydrogen bonds: A:Q.43, A:R.67, A:D.88, A:D.88 Salt bridges: A:K.45, A:K.51 ACT.4: 4 residues within 4Å: Chain A: S.120, V.121, K.213 Chain B: S.147 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:T.146, A:K.213 Hydrogen bonds: A:V.121 Salt bridges: A:K.213 ACT.5: 1 residues within 4Å: Chain B: N.219 No protein-ligand interaction detected (PLIP) ACT.6: 8 residues within 4Å: Chain A: S.168, S.182 Chain B: F.181, P.182, V.184, S.192, L.193, S.194 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.181, B:L.193 Hydrogen bonds: B:P.182, B:V.184, B:S.194, A:S.168, A:S.182 Water bridges: A:T.184

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

PGE.7: 8 residues within 4Å: Chain A: Y.97, N.99, Y.100, I.102 Chain B: N.59, Y.110, R.111, Y.112 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.109, B:R.111, B:Y.112, A:N.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bowers, P.M. et al., Nucleotide insertions and deletions complement point mutations to massively expand the diversity created by somatic hypermutation of antibodies. J.Biol.Chem. (2014)

Release Date

2014-10-22

Peptides

APE1531 Ab Fab light chain: A
APE1531 Ab Fab heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

APE1531 Ab Fab light chain

APE1531 Ab Fab heavy chain

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