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Cryo-EM structure of photorhabdus luminescens TCDA4

Analyse Cryo-EM structure of photorhabdus luminescens TCDA4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RWA
Type: protein
Length: 11,805 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TCDA4
UniProt: Q8GF92
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 1 distinct chain · 44% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	TCDA4	protein	2361	44% helix, 14% strand	Q8GF92

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	1080	0.86	0.87	130	empty
2	1105	0.86	0.87	129	empty
3	993	0.85	0.86	105	empty
4	1127	0.84	0.85	119	empty
5	778	0.84	0.87	92	empty

Interfaces

10 interfaces between chains.

A–E · 11010 Å² buried · 91 hydrogen bonds · protein-protein
A–B · 10988 Å² buried · 83 hydrogen bonds · protein-protein
B–C · 10971 Å² buried · 84 hydrogen bonds · protein-protein
D–E · 10957 Å² buried · 81 hydrogen bonds · protein-protein
C–D · 10948 Å² buried · 81 hydrogen bonds · protein-protein

Compared structures

6RWA · Cryo-EM structure of Photorhabdus luminescens TcdA4 · 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 Q8GF92
Elsewhere: RCSB PDB 6RWA · PDBe 6RWA · UniProt Q8GF92

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