MolNFT v1 · #149558 · protein

Crystal structure of semet-labeled mavirus penton protein

6G41 · Minor capsid protein: “Crystal structure of semet-labeled mavirus penton protein”. X-ray diffraction, 20 pockets (best druggability 0.73). MolNFT v1 #149558 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6G41
Type: protein
Length: 2,976 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Minor capsid protein
UniProt: A0A1L4BKA3
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 5 distinct chains · 14% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Minor capsid protein	protein	297	15% helix, 40% strand	A0A1L4BKA3
B	Minor capsid protein	protein	295	14% helix, 40% strand	A0A1L4BKA3
C, E, F, H, I, J	Minor capsid protein	protein	301	13% helix, 40% strand	A0A1L4BKA3
D	Minor capsid protein	protein	291	15% helix, 41% strand	A0A1L4BKA3
G	Minor capsid protein	protein	287	12% helix, 41% strand	A0A1L4BKA3

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	978	0.73	0.77	81	empty
2	407	0.71	0.82	51	empty
3	439	0.71	0.82	55	empty
4	376	0.70	0.82	45	empty
5	371	0.69	0.82	49	empty

Interfaces

18 interfaces between chains.

F–J · 2396 Å² buried · 35 hydrogen bonds · protein-protein
H–I · 2278 Å² buried · 37 hydrogen bonds · protein-protein
A–E · 2265 Å² buried · 29 hydrogen bonds · protein-protein
B–C · 2242 Å² buried · 39 hydrogen bonds · protein-protein
A–B · 2238 Å² buried · 37 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 40 modified (engineered).

Compared structures

6G41 · Crystal structure of SeMet-labeled mavirus penton protein · the same entry in another collection · chain A against A, 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 A0A1L4BKA3
Elsewhere: RCSB PDB 6G41 · PDBe 6G41 · UniProt A0A1L4BKA3

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