MolNFT v1 · #138416 · protein

Trae protein in complex with 2-chloroisonicotinic acid

5WII · Conjugal transfer protein: “Trae protein in complex with 2-chloroisonicotinic acid”. X-ray diffraction, 1 ligand (AO4), 13 pockets (best druggability 0.49). MolNFT v1 #138416 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5WII
Type: protein
Length: 560 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Conjugal transfer protein
UniProt: Q17U16
Ligands: AO4
Pockets: 13 · best druggability 0.49

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Conjugal transfer protein	protein	141	31% helix, 33% strand	Q17U16
B	Conjugal transfer protein	protein	143	32% helix, 34% strand	Q17U16
C	Conjugal transfer protein	protein	136	35% helix, 34% strand	Q17U16
D	Conjugal transfer protein	protein	140	30% helix, 33% strand	Q17U16

Ligands and binding sites

AO4 · 2-chloropyridine-4-carboxylic acid · ligand · chains A

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

Pockets

13 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	196	0.49	0.76	33	empty
2	139	0.49	0.78	26	AO4
3	96	0.46	0.80	18	empty
4	115	0.45	0.78	24	empty
5	213	0.45	0.73	19	empty

Interfaces

5 interfaces between chains.

B–D · 664 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 561 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 141 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 123 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 42 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5WII · TraE protein in complex with 2-Chloroisonicotinic Acid · 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 Q17U16
Elsewhere: RCSB PDB 5WII · PDBe 5WII · UniProt Q17U16

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