MolNFT v1 · #126659 · protein

Structure of the two C-terminal domains of bacteriophage K GP144

5M9F · ORF68: “Structure of the two C-terminal domains of bacteriophage K GP144”. X-ray diffraction, 1 ligand (NA), 8 pockets (best druggability 0.89). MolNFT v1 #126659 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5M9F
Type: protein
Length: 634 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ORF68
UniProt: Q6Y7P9
Ligands: NA
Pockets: 8 · best druggability 0.89

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ORF68	protein	212	8% helix, 53% strand	Q6Y7P9
C	ORF68	protein	210	10% helix, 54% strand	Q6Y7P9

Ligands and binding sites

NA · Sodium ion · metal · chains A, B, C
ACT · Acetate ion · additive · 5 copies · chains A, C, B

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	434	0.89	0.97	55	ACT
2	220	0.63	0.83	35	empty
3	86	0.38	0.77	22	empty
4	90	0.38	0.76	22	empty
5	50	0.34	0.79	13	empty

Interfaces

3 interfaces between chains.

A–B · 1667 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 1646 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 1539 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

5M9F · Structure of the two C-terminal domains of bacteriophage K gp144 · 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 Q6Y7P9
Elsewhere: RCSB PDB 5M9F · PDBe 5M9F · UniProt Q6Y7P9

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