SMTL ID : 6xr0.1

Crystal Structure of Human Melanotransferrin in complex with SC57.32 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.06 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain C: H.34, G.37, N.38, Y.318 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: G.55, G.56, N.57, T.58 Chain C: G.472, N.515 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.55, A:T.58, A:T.58, A:T.58

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 5 residues within 4Å: Chain C: E.84, K.87, E.88, I.134, N.135 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.134 Hydrogen bonds: C:K.87, C:K.87, C:N.135

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain C: D.503, D.505 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.505, C:D.505

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

NA.5: 3 residues within 4Å: Chain C: D.652, F.661, D.675 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.652

1 x FE: FE (III) ION(Non-covalent)

FE.6: 5 residues within 4Å: Chain C: D.78, Y.107, Y.210, H.279 Ligands: BCT.7 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.78, C:Y.107, C:Y.210, C:H.279

1 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.7: 10 residues within 4Å: Chain C: D.78, Y.107, T.132, R.136, T.137, V.138, G.139, D.209, Y.210 Ligands: FE.6 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.132, C:V.138, C:G.139, C:Y.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hayashi, K. et al., Complex of human Melanotransferrin and SC57.32 Fab fragment reveals novel interdomain arrangement with ferric N-lobe and open C-lobe. Sci Rep (2021)

Release Date

2021-01-20

Peptides

SC57.32 Fab Heavy Chain: A
SC57.32 Fab Light Chain: B
Melanotransferrin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
M

SC57.32 Fab Heavy Chain

SC57.32 Fab Light Chain

Melanotransferrin