SMTL ID : 2gtb.1

Crystal structure of SARS coronavirus main peptidase (with an additional Ala at the N-terminus of each protomer) inhibited by an aza-peptide epoxide in the space group P43212

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x AZP: (5S,8S,14R)-ETHYL 11-(3-AMINO-3-OXOPROPYL)-8-BENZYL-14-HYDROXY-5-ISOBUTYL-3,6,9,12-TETRAOXO-1-PHENYL-2-OXA-4,7,10,11-TETRAAZAPENTADECAN-15-OATE(Non-covalent)

AZP.1: 23 residues within 4Å: Chain A: T.26, H.42, M.50, Y.55, F.141, L.142, N.143, G.144, S.145, C.146, H.164, H.165, M.166, E.167, L.168, P.169, H.173, D.188, R.189, Q.190, T.191, Q.193, A.194 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:H.42, A:M.50, A:L.168, A:P.169, A:Q.190, A:Q.193 Hydrogen bonds: A:N.143, A:G.144, A:S.145, A:S.145, A:C.146, A:H.165, A:E.167, A:E.167, A:E.167, A:Q.190 Salt bridges: A:H.42 pi-Stacking: A:H.42 AZP.3: 23 residues within 4Å: Chain B: T.26, H.42, M.50, Y.55, F.141, L.142, N.143, G.144, S.145, C.146, H.164, H.165, M.166, E.167, L.168, P.169, H.173, D.188, R.189, Q.190, T.191, Q.193, A.194 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:H.42, B:M.50, B:L.168, B:P.169, B:Q.190, B:Q.193 Hydrogen bonds: B:N.143, B:G.144, B:S.145, B:S.145, B:C.146, B:H.165, B:E.167, B:E.167, B:E.167, B:Q.190 Salt bridges: B:H.42 pi-Stacking: B:H.42

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.2: 5 residues within 4Å: Chain A: K.6, A.8, V.126, Y.127, Q.128 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.8 Hydrogen bonds: A:Q.128 ACY.4: 5 residues within 4Å: Chain B: K.6, A.8, V.126, Y.127, Q.128 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.8 Hydrogen bonds: B:Q.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, T.W. et al., Crystal Structures Reveal an Induced-fit Binding of a Substrate-like Aza-peptide Epoxide to SARS Coronavirus Main Peptidase. J.Mol.Biol. (2007)

Release Date

2006-12-26

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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