SMTL ID : 1lvo.1 (3 other biounits)

Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: N.168, L.192, E.193, G.194 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.168, A:E.193, A:G.194 Water bridges: A:N.168, A:N.168 SO4.2: 3 residues within 4Å: Chain A: R.130, K.136, N.196 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.196 Salt bridges: A:R.130, A:K.136 SO4.3: 4 residues within 4Å: Chain A: G.214, E.215, R.216, W.217 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.214, A:R.216, A:W.217 Water bridges: A:W.217 SO4.4: 2 residues within 4Å: Chain A: K.103, S.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.104 Water bridges: A:E.177 SO4.5: 4 residues within 4Å: Chain A: R.19, S.21, V.26, S.66 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.21, A:S.21, A:S.66 Salt bridges: A:R.19 SO4.10: 4 residues within 4Å: Chain B: N.168, L.192, E.193, G.194 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.168, B:E.193, B:G.194 Water bridges: B:N.168 SO4.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.12: 3 residues within 4Å: Chain B: K.82, F.102, F.176 No protein-ligand interaction detected (PLIP) SO4.13: 3 residues within 4Å: Chain B: R.19, S.21, S.66 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.21, B:S.66 Water bridges: B:R.19, B:S.66 Salt bridges: B:R.19

4 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.6: 6 residues within 4Å: Chain A: M.6, Q.8, S.110, F.111, N.112, E.291 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.8 DIO.7: 6 residues within 4Å: Chain A: A.107, M.129, R.130, S.131, Q.132, G.133 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.182 DIO.8: 2 residues within 4Å: Chain A: G.122, S.123 No protein-ligand interaction detected (PLIP) DIO.14: 7 residues within 4Å: Chain B: F.139, I.140, A.141, C.144, H.162, L.164, E.165 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.165

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.9: 6 residues within 4Å: Chain A: H.41, T.47, H.163, L.164, Q.187, P.188 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.41, A:T.47, A:P.188 Water bridges: A:E.165 MRD.15: 8 residues within 4Å: Chain B: H.41, T.47, I.51, Y.53, L.164, D.186, Q.187, P.188 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:H.41, B:L.164, B:L.164, B:D.186 Hydrogen bonds: B:T.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anand, K. et al., Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain. EMBO J. (2002)

Release Date

2002-07-17

Peptides

Replicase, hydrolase domain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Replicase, hydrolase domain

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