SMTL ID : 7d9z.1

Crystal structure of anti-basigin Fab fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: Y.33, Y.92, Y.93, A.94 Chain B: Y.95 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Y.95 Hydrogen bonds: A:A.94 EDO.2: 3 residues within 4Å: Chain B: N.203, T.204, K.205 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.205 Water bridges: B:K.205 EDO.3: 2 residues within 4Å: Chain B: T.190, Q.191 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.191 EDO.4: 12 residues within 4Å: Chain A: Y.37, Q.90, T.91, Y.92, I.95, A.100 Chain B: S.34, W.46, I.49, Y.95, G.98, S.99 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.37, A:Y.37, A:Q.90, B:S.34, B:W.46, B:S.99 Water bridges: B:S.34 EDO.5: 6 residues within 4Å: Chain B: R.37, W.61, R.65, F.66, E.85, D.86 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.37, B:R.37, B:D.86 Water bridges: B:R.65 EDO.6: 6 residues within 4Å: Chain B: G.8, R.9, L.10, T.115, P.146, P.201 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.10 Water bridges: B:L.10

1 x FLC: CITRATE ANION(Non-covalent)

FLC.7: 5 residues within 4Å: Chain B: P.13, T.84, S.111, S.112, A.113 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:T.84 Hydrogen bonds: B:S.112, B:S.112 Water bridges: B:T.84, B:T.84, B:T.84, B:S.111, B:S.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakuragi, T. et al., The tertiary structure of the human Xkr8-Basigin complex that scrambles phospholipids at plasma membranes. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-10-20

Peptides

Light chain of antibody Fab fragment: A
Heavy chain of antibody Fab fragment: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

Light chain of antibody Fab fragment

Heavy chain of antibody Fab fragment

Related Entries With Identical Sequence