MolNFT v1 · #5171 · protein

Bacterial conjugative coupling protein TRWBDELTAN70. trigonal form in complex with sulphate.

1E9R · Conjugal transfer protein trwb: “Bacterial conjugative coupling protein TRWBDELTAN70. trigonal form in complex with sulphate.”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.87). MolNFT v1 #5171 on GenesisL1: 3D…

PDB: 1E9R
Type: protein
Length: 2,509 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Conjugal transfer protein trwb
UniProt: Q04230
Ligands: SO4
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 6 distinct chains · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Conjugal transfer protein trwb	protein	420	44% helix, 18% strand	Q04230
B	Conjugal transfer protein trwb	protein	422	43% helix, 18% strand	Q04230
D	Conjugal transfer protein trwb	protein	415	45% helix, 18% strand	Q04230
E	Conjugal transfer protein trwb	protein	419	44% helix, 18% strand	Q04230
F	Conjugal transfer protein trwb	protein	416	44% helix, 19% strand	Q04230
G	Conjugal transfer protein trwb	protein	417	44% helix, 18% strand	Q04230

Ligands and binding sites

SO4 · Sulfate ion · ion · 15 copies · chains A, B, D, E, F, G

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1094	0.87	0.88	113	SO4
2	1170	0.87	0.88	113	SO4
3	1131	0.87	0.88	110	SO4
4	1087	0.87	0.88	104	SO4
5	1105	0.86	0.87	106	SO4

Interfaces

6 interfaces between chains.

A–B · 2516 Å² buried · 36 hydrogen bonds · protein-protein
B–D · 2469 Å² buried · 25 hydrogen bonds · protein-protein
F–G · 2467 Å² buried · 29 hydrogen bonds · protein-protein
A–G · 2462 Å² buried · 34 hydrogen bonds · protein-protein
E–F · 2422 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

1E9R · Bacterial conjugative coupling protein TrwBdeltaN70. Trigonal form in complex with… · 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 Q04230
Elsewhere: RCSB PDB 1E9R · PDBe 1E9R · UniProt Q04230

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