SMTL ID : 8v04.1

High resolution TMPRSS2 structure following acylation by nafamostat

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG-FUC.1: 8 residues within 4Å: Chain A: N.68, S.70, A.71, V.74, K.78, Y.81 Ligands: EDO.2, EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.71, A:V.74 Hydrogen bonds: A:G.72

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

EDO.2: 2 residues within 4Å: Chain A: Y.81 Ligands: NAG-NAG-NAG-FUC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.81 EDO.4: 1 residues within 4Å: Chain A: S.70 No protein-ligand interaction detected (PLIP) EDO.5: 7 residues within 4Å: Chain A: N.68, K.78, K.79, L.80, Y.81 Ligands: NAG-NAG-NAG-FUC.1, NAG-NAG-NAG-FUC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.78 EDO.9: 4 residues within 4Å: Chain B: P.9, G.58, L.60, L.105 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.58 Water bridges: B:G.10 EDO.10: 6 residues within 4Å: Chain A: D.42, M.43 Chain B: D.227, Y.230, R.231, R.234 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.227, A:D.42 Water bridges: B:D.227 EDO.11: 4 residues within 4Å: Chain B: G.58, N.103, L.105, V.106 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.58, B:N.103 EDO.13: 1 residues within 4Å: Chain B: Y.159 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.214, B:Y.214 EDO.14: 2 residues within 4Å: Chain B: V.76, I.77 3 PLIP interactions: 3 interactions with chain B Water bridges: B:V.76, B:V.76, B:V.76 EDO.15: 4 residues within 4Å: Chain B: A.69, G.70, Y.71, K.98 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.70

1 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 1 residues within 4Å: Chain A: C.3 No protein-ligand interaction detected (PLIP)

1 x GBS: 4-carbamimidamidobenzoic acid(Covalent)

GBS.6: 16 residues within 4Å: Chain B: D.180, S.181, C.182, Q.183, G.184, D.185, S.186, T.204, S.205, W.206, G.207, G.209, C.210, R.215, P.216, G.217 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.204 Hydrogen bonds: B:S.181, B:S.181, B:G.184, B:D.185, B:S.186, B:S.208 Water bridges: B:D.180, B:W.206, B:G.209 Salt bridges: B:D.180

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.7: 3 residues within 4Å: Chain B: Q.176, G.177, N.178 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.176, B:N.178

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 1 residues within 4Å: Chain B: N.48 No protein-ligand interaction detected (PLIP)

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

PG4.12: 7 residues within 4Å: Chain B: K.85, T.86, K.87, L.164, T.166, M.169, W.206 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fraser, B.J. et al., High resolution TMPRSS2 structure following acylation by nafamostat. To Be Published

Release Date

2024-01-31

Peptides

Transmembrane protease serine 2 non-catalytic chain: A
Transmembrane protease serine 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transmembrane protease serine 2 non-catalytic chain

Transmembrane protease serine 2

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