MolNFT v1 · #67849 · protein

The octameric SARS-cov main protease

3IWM · 3C-like proteinase: “The octameric SARS-cov main protease”. X-ray diffraction, 3 ligands (02J, PJE, 010), 16 pockets (best druggability 0.76). MolNFT v1 #67849 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3IWM
Type: protein
Length: 1,214 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase; N-[(5-methylisoxazol-3-YL)CARBONYL]ALANYL-L-valyl-N~1~…
EC: 3.4.22.-
UniProt: P0C6U8
Ligands: 02J, PJE, 010
Pockets: 16 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 21% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	3C-like proteinase (EC 3.4.22.-)	protein	301	22% helix, 23% strand	P0C6U8
C, D	3C-like proteinase (EC 3.4.22.-)	protein	300	20% helix, 25% strand	P0C6U8
H, F, G, E	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	protein	3	0% helix, 0% strand	—

Ligands and binding sites

02J · 5-methyl-1,2-oxazole-3-carboxylic acid · ligand · 4 copies · chains A, H, B, F, C, G, D, E
PJE · (E,4S)-4-azanyl-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pent-2-enoic acid · ligand · 4 copies · chains A, B, H, F, C, G, D, E
010 · phenylmethanol · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

16 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	940	0.76	0.79	74	empty
2	313	0.68	0.83	30	empty
3	163	0.50	0.78	27	PJE, 010
4	171	0.50	0.77	27	PJE, 010
5	212	0.49	0.75	42	empty

Interfaces

10 interfaces between chains.

A–C · 4367 Å² buried · 49 hydrogen bonds · protein-protein
B–D · 4318 Å² buried · 43 hydrogen bonds · protein-protein
A–B · 1047 Å² buried · 28 hydrogen bonds · protein-protein
C–G · 327 Å² buried · 5 hydrogen bonds · protein-protein
B–F · 323 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

3IWM · The octameric SARS-CoV main protease · the same entry in another collection · chain E against E, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P0C6U8
Elsewhere: RCSB PDB 3IWM · PDBe 3IWM · UniProt P0C6U8

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