MolNFT v1 · #140452 · protein

Dimeric cyclophilin from T.VAGINALIS in complex with MYB1 peptide

5YBA: “Dimeric cyclophilin from T.VAGINALIS in complex with MYB1 peptide”. X-ray diffraction, 1 pocket (best druggability 0.57). MolNFT v1 #140452 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YBA
Type: protein
Length: 358 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MYB1 peptide; Peptidyl-prolyl cis-trans isomerase
EC: 5.2.1.8
UniProt: A2DT06
Pockets: 1 · best druggability 0.57

Structure

x-ray diffraction · 4 distinct chains · 13% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	MYB1 peptide	protein	6	0% helix, 0% strand	—
A	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8)	protein	172	13% helix, 32% strand	A2DT06
D	MYB1 peptide	protein	5	0% helix, 0% strand	—
C	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8)	protein	175	13% helix, 33% strand	A2DT06

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	223	0.57	0.79	31	empty

Interfaces

3 interfaces between chains.

A–C · 918 Å² buried · 11 hydrogen bonds · protein-protein
B–A · 502 Å² buried · 9 hydrogen bonds · protein-protein
D–C · 350 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5YBA · Dimeric Cyclophilin from T.vaginalis in complex with Myb1 peptide · the same entry in another collection · chain B against B, 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 A2DT06
Elsewhere: RCSB PDB 5YBA · PDBe 5YBA · UniProt A2DT06

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