SMTL ID : 8oju.1

Crystal structure of the human IgD Fab - structure Fab3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-1-1-mer

Ligands

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 7 residues within 4Å: Chain A: S.126, S.127 Chain B: P.131, P.222, E.223, S.224, P.225 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.127, B:P.131 EDO.2: 4 residues within 4Å: Chain A: N.53, N.54, S.67, K.68 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.53, A:K.68 Water bridges: A:N.54, A:N.54 EDO.3: 8 residues within 4Å: Chain A: S.119, V.120, T.121, L.140, I.141, S.142 Chain B: R.173, Q.190 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.121, A:S.142, B:Q.190 EDO.4: 4 residues within 4Å: Chain A: Y.33, F.93, W.100 Chain B: V.106 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.101 EDO.5: 5 residues within 4Å: Chain A: D.34, G.52, N.55 Chain B: Y.102, S.104 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.104, A:D.34 Water bridges: A:N.53 EDO.6: 3 residues within 4Å: Chain A: K.115, A.116, A.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.117 Water bridges: A:A.117 EDO.8: 3 residues within 4Å: Chain B: R.50, N.52, N.57 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.50, B:R.50, B:N.52 Water bridges: B:N.55 EDO.9: 5 residues within 4Å: Chain B: R.12, S.17, V.18, K.19, D.82 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.12, B:R.12, B:K.19, B:D.82 EDO.10: 2 residues within 4Å: Chain B: N.55, R.72 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.55, B:R.72, B:R.72 Water bridges: B:R.72, B:R.72

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

NA.7: 1 residues within 4Å: Chain A: Y.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.31 NA.12: 1 residues within 4Å: Chain B: K.204 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.204, B:K.204

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

PG4.11: 8 residues within 4Å: Chain B: T.162, Y.164, G.166, K.204, V.206, Q.208, K.215, E.217 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.162, B:Y.164, B:G.166, B:K.204, B:K.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davies, A.M. et al., Crystal structures of the human IgD Fab reveal insights into C H 1 domain diversity. Mol.Immunol. (2023)

Release Date

2023-06-14

Peptides

Human IgD Fab light chain: A
Human IgD Fab heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

Human IgD Fab light chain

Human IgD Fab heavy chain

Related Entries With Identical Sequence