SMTL ID : 9fik.1

Structure of the FAB fragment of the Antibody NTF30037 in complex with NTF3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

hetero-1-1-1-mer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: Q.34, V.35, T.36, S.91, E.92, N.93 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.34, A:T.36, A:T.36, A:N.93, A:N.93 Water bridges: A:S.26, A:Q.34, A:T.36 GOL.2: 4 residues within 4Å: Chain A: Q.83, T.84, Y.85, R.103 No protein-ligand interaction detected (PLIP) GOL.3: 5 residues within 4Å: Chain A: N.76, S.77, Q.78, L.112, S.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.77, A:L.112 Water bridges: A:S.77 GOL.4: 6 residues within 4Å: Chain B: F.27, T.100, S.101, G.102, D.120, Y.121 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.100, B:S.101 GOL.6: 5 residues within 4Å: Chain B: W.118, D.120 Chain C: Y.48, P.54, S.55 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.55 Water bridges: C:Y.48, C:Y.48

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

PEG.5: 8 residues within 4Å: Chain B: G.42, K.43 Chain C: D.84, Y.86, G.101, G.102, T.103, K.104 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.84 PEG.7: 3 residues within 4Å: Chain C: R.19, T.21, T.71 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.21 Hydrogen bonds: C:T.71 Water bridges: C:T.71

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 3 residues within 4Å: Chain C: L.108, P.143, E.200 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chin, S.E. et al., Identification of unique binding mode anti-NTF3 antibodies from a novel long VH CDR3 phage display library. Slas Discov (2025)

Release Date

2025-04-02

Peptides

Neurotrophin-3: A
NTF30037 Heavy Chain: B
NTF30037 Light Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Neurotrophin-3

NTF30037 Heavy Chain

NTF30037 Light Chain