MolNFT v1 · #68855 · protein

Structure of crystal form I of TP0453

3K8H · 30KLP: “Structure of crystal form I of TP0453”. X-ray diffraction, 7 pockets (best druggability 0.84). MolNFT v1 #68855 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3K8H
Type: protein
Length: 502 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 30KLP
UniProt: O67998
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	30KLP	protein	252	29% helix, 33% strand	O67998
B	30KLP	protein	250	30% helix, 32% strand	O67998

Ligands and binding sites

MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	199	0.84	0.97	24	MPD
2	570	0.82	0.87	40	empty
3	214	0.59	0.80	25	empty
4	276	0.54	0.76	42	empty
5	84	0.48	0.80	15	empty

Interfaces

1 interface between chains.

A–B · 328 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3K8H · 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 3K8H · PDBe 3K8H · UniProt O67998

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