SMTL ID : 7ara.1

Rhinovirus A2 2A protease in complex with zVAM.fmk

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-dimer

Ligands

1 x S7N: (phenylmethyl) ~{N}-[(2~{R})-3-methyl-1-[[(2~{S})-1-[[(3~{S})-1-methylsulfanyl-4-oxidanylidene-pentan-3-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate(Covalent)

S7N.1: 17 residues within 4Å: Chain A: H.18, Y.78, I.80, Q.81, E.82, S.83, Y.85, I.96, P.103, G.104, D.105, C.106, T.121, A.122, G.123, G.124, H.127 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.78, A:Y.85, A:I.96, A:H.127 Hydrogen bonds: A:H.18, A:Q.81, A:Y.85, A:G.104, A:D.105, A:C.106, A:G.123

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.52, C.54, C.112, H.114 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.52, A:C.54, A:C.112, A:H.114 ZN.4: 4 residues within 4Å: Chain B: C.52, C.54, C.112, H.114 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.52, B:C.54, B:C.112, B:H.114

1 x S7Q: (phenylmethyl) ~{N}-[(2~{S})-3-methyl-1-[[(2~{R})-1-[[(3~{R})-1-methylsulfanyl-4-oxidanylidene-pentan-3-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate(Covalent)

S7Q.3: 16 residues within 4Å: Chain B: H.18, Y.78, I.80, Q.81, S.83, I.96, C.101, E.102, P.103, G.104, C.106, T.121, A.122, G.123, G.124, H.127 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.78, B:I.80, B:Q.81, B:I.96, B:I.96, B:H.127 Hydrogen bonds: B:G.104, B:G.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deutschmann-Olek, K.M. et al., Defining substrate selection by rhinoviral 2A proteinase through its crystal structure with the inhibitor zVAM.fmk. Virology (2021)

Release Date

2021-07-28

Peptides

2A protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2A protease

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