SMTL ID : 6kd5.1

Crystal structure of the extracellular domain of MSPL/TMPRSS13 in complex with dec-RVKR-cmk inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

1 x DKA- ARG- VAL- LYS- AR7- 0QE: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR(Non-covalent)

DKA-ARG-VAL-LYS-AR7-0QE.1: 21 residues within 4Å: Chain B: H.41, Y.81, D.83, E.85, D.86, E.133, D.180, S.181, C.182, Q.183, G.184, D.185, S.186, S.205, W.206, G.207, T.208, G.209, Q.212, G.217 Ligands: SO4.11 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Q.183, B:W.206, B:T.208 Hydrogen bonds: B:D.86, B:S.181, B:S.181, B:Q.183, B:G.184, B:D.185, B:S.186, B:S.205, B:G.207, B:G.209, B:G.209 Salt bridges: B:D.180

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 3 residues within 4Å: Chain A: N.86, S.88, K.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.88

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

NAG-NAG.3: 6 residues within 4Å: Chain B: N.78, S.79, N.80, Y.88, W.228 Ligands: SO4.9 No protein-ligand interaction detected (PLIP)

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: R.151, A.152, M.153, T.154 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.154 Water bridges: A:R.151, A:R.151 Salt bridges: A:R.151 SO4.5: 5 residues within 4Å: Chain A: C.81, S.83, S.118, H.131, S.133 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.83, A:S.83, A:S.118, A:S.133 Water bridges: A:E.134, A:C.135 Salt bridges: A:H.131 SO4.6: 5 residues within 4Å: Chain A: S.71, G.72, S.73, F.117, R.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.72, A:S.73, A:S.73 SO4.8: 3 residues within 4Å: Chain B: D.135, D.136, K.137 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.136, B:D.136, B:K.137 SO4.9: 2 residues within 4Å: Chain B: R.168 Ligands: NAG-NAG.3 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.168 SO4.10: 3 residues within 4Å: Chain B: F.44, K.49, D.83 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.83, B:D.83 Salt bridges: B:K.49 SO4.11: 3 residues within 4Å: Ligands: DKA-ARG-VAL-LYS-AR7-0QE.1, DKA-ARG-VAL-LYS-AR7-0QE.1, DKA-ARG-VAL-LYS-AR7-0QE.1 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 6 residues within 4Å: Chain A: V.40, D.43, V.45, D.47, D.53, E.54 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:V.40, A:D.43, A:V.45, A:D.47, A:D.53, A:E.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ohno, A. et al., Crystal structure of inhibitor-bound human MSPL that can activate high pathogenic avian influenza. Life Sci Alliance (2021)

Release Date

2020-06-24

Peptides

Transmembrane protease serine 13: A
Transmembrane protease serine 13: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transmembrane protease serine 13

Transmembrane protease serine 13