MolNFT v1 · #135794 · protein

Cocrystal structure of the intermembrane space region of the plastid division proteins PARC6 and PDV1

5U9O · Plastid division protein CDP1, CHLOROPLASTIC,PLASTID…: “Cocrystal structure of the intermembrane space region of the plastid division proteins PARC6 and PDV1”. X-ray diffraction, 9 pockets (best druggability 0.82). MolNFT v1 #135794…

PDB: 5U9O
Type: protein
Length: 1,145 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1
UniProt: Q8VY16, Q9FK13
Pockets: 9 · best druggability 0.82

Structure

x-ray diffraction · 8 distinct chains · 29% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	145	28% helix, 38% strand	Q8VY16, Q9FK13
B	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	144	28% helix, 43% strand	Q8VY16, Q9FK13
C	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	145	29% helix, 39% strand	Q8VY16, Q9FK13
D	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	146	29% helix, 40% strand	Q8VY16, Q9FK13
E	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	144	27% helix, 38% strand	Q8VY16, Q9FK13
F	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	142	30% helix, 39% strand	Q8VY16, Q9FK13
G	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	139	29% helix, 43% strand	Q8VY16, Q9FK13
H	Plastid division protein CDP1, CHLOROPLASTIC,PLASTID division protein PDV1	protein	140	28% helix, 37% strand	Q8VY16, Q9FK13

Pockets

9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	909	0.82	0.84	79	empty
2	211	0.73	0.89	30	empty
3	431	0.70	0.81	44	empty
4	312	0.66	0.82	40	empty
5	191	0.60	0.82	27	empty

Interfaces

14 interfaces between chains.

E–H · 1061 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1048 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 732 Å² buried · 5 hydrogen bonds · protein-protein
A–H · 690 Å² buried · 12 hydrogen bonds · protein-protein
A–G · 576 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5U9O · Cocrystal structure of the intermembrane space region of the plastid division proteins… · the same entry in another collection · chain B against B, TM-score 1.00
Q8VY16 · AlphaFold monomer V2.0 prediction for plastid division protein CDP1, chloroplastic… · a predicted model of the same protein · chain G against A, TM-score 0.91

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 Q8VY16
Every structure of UniProt Q9FK13
Elsewhere: RCSB PDB 5U9O · PDBe 5U9O · UniProt Q8VY16 · UniProt Q9FK13

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