MolNFT v1 · #135109 · protein

The structure of the C-terminus of virulence protein ince from chlamydia trachomatis bound to mus musculus SNX5-px domain

5TP1 · Sorting nexin-5: “The structure of the C-terminus of virulence protein ince from chlamydia trachomatis bound to mus musculus…”. X-ray diffraction, 6 pockets (best druggability 0.42). MolNFT v1 #135109 on GenesisL1: 3D structure…

PDB: 5TP1
Type: protein
Length: 691 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sorting nexin-5; Inclusion membrane protein E
UniProt: Q9D8U8, P0DJI4
Pockets: 6 · best druggability 0.42

Structure

x-ray diffraction · 5 distinct chains · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Sorting nexin-5	protein	150	46% helix, 17% strand	Q9D8U8
C, D	Sorting nexin-5	protein	155	48% helix, 17% strand	Q9D8U8
P, Q	Inclusion membrane protein E	protein	21	0% helix, 43% strand	P0DJI4
R	Inclusion membrane protein E	protein	19	0% helix, 47% strand	P0DJI4
S	Inclusion membrane protein E	protein	20	15% helix, 40% strand	P0DJI4

Pockets

6 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	76	0.42	0.80	15	empty
2	100	0.37	0.75	16	empty
3	71	0.34	0.76	18	empty
4	55	0.30	0.75	14	empty
5	56	0.28	0.74	19	empty

Interfaces

7 interfaces between chains.

A–P · 709 Å² buried · 8 hydrogen bonds · protein-protein
D–S · 699 Å² buried · 9 hydrogen bonds · protein-protein
B–Q · 678 Å² buried · 7 hydrogen bonds · protein-protein
C–R · 677 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 632 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5TP1 · The structure of the C-terminus of virulence protein IncE from Chlamydia trachomatis… · the same entry in another collection · chain Q against Q, TM-score 1.00
Q9D8U8 · AlphaFold monomer V2.0 prediction for sorting nexin-5 (Q9D8U8) · a predicted model of the same protein · chain A against A, TM-score 0.94
P0DJI4 · AlphaFold monomer V2.0 prediction for inclusion membrane protein E (P0DJI4) · a predicted model of the same protein · chain S against A, TM-score 0.27

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 Q9D8U8
Every structure of UniProt P0DJI4
Elsewhere: RCSB PDB 5TP1 · PDBe 5TP1 · UniProt Q9D8U8 · UniProt P0DJI4

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