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Cryo-EM structure of photorhabdus luminescens TCDA1

Analyse Cryo-EM structure of photorhabdus luminescens TCDA1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RW6
Type: protein
Length: 12,425 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TCDA1
UniProt: Q9RN43
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 1 distinct chain · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	TCDA1	protein	2485	43% helix, 18% strand	Q9RN43

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	919	0.86	0.88	114	empty
2	907	0.86	0.88	122	empty
3	831	0.86	0.88	100	empty
4	875	0.85	0.87	96	empty
5	846	0.85	0.87	94	empty

Interfaces

10 interfaces between chains.

A–B · 12181 Å² buried · 135 hydrogen bonds · protein-protein
B–C · 12105 Å² buried · 122 hydrogen bonds · protein-protein
A–E · 12096 Å² buried · 128 hydrogen bonds · protein-protein
D–E · 12095 Å² buried · 129 hydrogen bonds · protein-protein
C–D · 12088 Å² buried · 128 hydrogen bonds · protein-protein

Compared structures

6RW6 · Cryo-EM structure of Photorhabdus luminescens TcdA1 · 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 Q9RN43
Elsewhere: RCSB PDB 6RW6 · PDBe 6RW6 · UniProt Q9RN43

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