SMTL ID : 3iwm.1

The octameric SARS-CoV main protease

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-octamer

Ligands

8 x 02J- ALA- VAL- LEU- PJE- 010: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE(Non-covalent)

02J-ALA-VAL-LEU-PJE-010.1: 22 residues within 4Å: Chain A: T.24, T.25, T.26, L.27, H.41, F.140, L.141, N.142, G.143, C.145, H.163, H.164, M.165, E.166, L.167, P.168, D.187, R.188, Q.189, T.190, A.191, Q.192 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.41, A:P.168, A:Q.192 Hydrogen bonds: A:G.143, A:C.145, A:H.164, A:E.166, A:E.166, A:E.166, A:Q.189 Salt bridges: A:H.41 02J-ALA-VAL-LEU-PJE-010.2: 19 residues within 4Å: Chain B: T.24, T.25, T.26, H.41, Y.54, F.140, N.142, G.143, C.145, H.163, H.164, M.165, E.166, P.168, H.172, D.187, Q.189, T.190, Q.192 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.25, B:M.165, B:P.168, B:D.187, B:Q.192 Hydrogen bonds: B:E.166, B:E.166, B:E.166, B:Q.189, B:T.190 02J-ALA-VAL-LEU-PJE-010.3: 22 residues within 4Å: Chain C: T.25, L.27, H.41, M.49, F.140, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, A.191 Chain H: S.1 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:N.142, C:P.168, C:Q.189 Hydrogen bonds: C:G.143, C:C.145, C:E.166, C:E.166, C:E.166, C:Q.189, C:T.190 Salt bridges: C:H.41 02J-ALA-VAL-LEU-PJE-010.4: 23 residues within 4Å: Chain D: T.26, L.27, H.41, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, A.191, Q.192 Chain G: S.1 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:N.142, D:A.191 Hydrogen bonds: D:G.143, D:C.145, D:E.166, D:E.166, D:E.166, D:Q.189 02J-ALA-VAL-LEU-PJE-010.5: 22 residues within 4Å: Chain E: T.24, T.25, T.26, L.27, H.41, F.140, L.141, N.142, G.143, C.145, H.163, H.164, M.165, E.166, L.167, P.168, D.187, R.188, Q.189, T.190, A.191, Q.192 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:H.41, E:P.168, E:Q.192 Hydrogen bonds: E:G.143, E:C.145, E:H.164, E:E.166, E:E.166, E:Q.189 Salt bridges: E:H.41 02J-ALA-VAL-LEU-PJE-010.6: 19 residues within 4Å: Chain F: T.24, T.25, T.26, H.41, Y.54, F.140, N.142, G.143, C.145, H.163, H.164, M.165, E.166, P.168, H.172, D.187, Q.189, T.190, Q.192 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:T.25, F:M.165, F:P.168, F:D.187, F:Q.192 Hydrogen bonds: F:E.166, F:E.166, F:E.166, F:E.166, F:Q.189, F:T.190 02J-ALA-VAL-LEU-PJE-010.7: 22 residues within 4Å: Chain D: S.1 Chain G: T.25, L.27, H.41, M.49, F.140, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, A.191 12 PLIP interactions: 1 interactions with chain D, 11 interactions with chain G Hydrogen bonds: D:S.1, G:G.143, G:C.145, G:E.166, G:E.166, G:E.166, G:Q.189, G:T.190 Hydrophobic interactions: G:N.142, G:P.168, G:Q.189 Salt bridges: G:H.41 02J-ALA-VAL-LEU-PJE-010.8: 23 residues within 4Å: Chain C: S.1 Chain H: T.26, L.27, H.41, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, A.191, Q.192 10 PLIP interactions: 9 interactions with chain H, 1 interactions with chain C Hydrophobic interactions: H:N.142, H:A.191 Hydrogen bonds: H:G.143, H:C.145, H:E.166, H:E.166, H:E.166, H:E.166, H:Q.189, C:S.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S. et al., Three-dimensional domain swapping as a mechanism to lock the active conformation in a super-active octamer of SARS-CoV main protease. Protein Cell (2010)

Release Date

2010-07-21

Peptides

3C-like proteinase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

3C-like proteinase

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