SMTL ID : 9jd1.1

Crystal structure of TMPRSS2 in complex with Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 4 residues within 4Å: Chain B: N.105, S.107, A.108, Y.118 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain B: N.23, D.26, V.28, H.30, D.36, E.37 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:N.23, B:D.26, B:V.28, B:H.30, B:D.36, B:E.37

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

MES.3: 5 residues within 4Å: Chain C: T.23, R.24, S.25, G.27, N.72 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.72 Water bridges: C:G.27

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: N.22, S.63, M.65, F.66, Y.67 Chain C: R.111, A.114, D.173 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:N.22, A:N.22, A:S.63, A:Y.67, C:R.111, C:R.111, C:D.173, C:D.173 GOL.5: 4 residues within 4Å: Chain D: N.54, R.72, D.73, N.74 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.74 Water bridges: D:R.72, D:N.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Z. et al., The crystal structure of coronavirus RBD-TMPRSS2 complex provides basis for the discovery of therapeutic antibodies. Nat Commun (2025)

Release Date

2025-07-30

Peptides

Transmembrane protease serine 2 catalytic chain: A
Transmembrane protease serine 2 non-catalytic chain: B
Light chain of Fab: C
Heavy chain of Fab: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
A

D
B

Transmembrane protease serine 2 catalytic chain

Transmembrane protease serine 2 non-catalytic chain

Light chain of Fab

Heavy chain of Fab

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