MolNFT v1 · #68854 · protein

Structure of crystal form I of TP0453

3K8G · 30KLP: “Structure of crystal form I of TP0453”. X-ray diffraction, 8 pockets (best druggability 0.79). MolNFT v1 #68854 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3K8G
Type: protein
Length: 489 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 30KLP
UniProt: O67998
Pockets: 8 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	30KLP	protein	251	29% helix, 33% strand	O67998
B	30KLP	protein	238	26% helix, 34% strand	O67998

Ligands and binding sites

MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	249	0.79	0.91	34	MPD
2	304	0.71	0.84	36	MPD
3	350	0.60	0.77	44	empty
4	216	0.57	0.79	35	empty
5	156	0.54	0.80	22	empty

Interfaces

1 interface between chains.

A–B · 898 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

3K8G · Structure of crystal form I of TP0453 · the same entry in another collection · chain A against A, TM-score 1.00
O67998 · AlphaFold monomer V2.0 prediction for outer membrane protein TP0453 (O67998) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O67998
Elsewhere: RCSB PDB 3K8G · PDBe 3K8G · UniProt O67998

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