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Crystal structure of yeast YER010CP

Analyse Crystal structure of yeast YER010CP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2C5Q
Type: protein
Length: 1,390 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rraa-like protein YER010C
UniProt: P40011
Pockets: 10 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Rraa-like protein YER010C	protein	232	32% helix, 28% strand	P40011
B	Rraa-like protein YER010C	protein	231	32% helix, 28% strand	P40011
E	Rraa-like protein YER010C	protein	233	34% helix, 28% strand	P40011
F	Rraa-like protein YER010C	protein	230	33% helix, 29% strand	P40011

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D, E, F

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

Pockets

10 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	803	0.74	0.79	68	EDO
2	800	0.74	0.79	67	EDO
3	855	0.74	0.78	76	EDO
4	681	0.73	0.80	54	empty
5	566	0.71	0.80	49	EDO

Interfaces

7 interfaces between chains.

E–F · 1339 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1329 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1321 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 1312 Å² buried · 17 hydrogen bonds · protein-protein
D–F · 1311 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (artifact).

Compared structures

2C5Q · Crystal structure of yeast YER010Cp · the same entry in another collection · chain F against F, TM-score 1.00
P40011 · AlphaFold monomer V2.0 prediction for 4-hydroxy-4-methyl-2-oxoglutarate aldolase (P40011) · a predicted model of the same protein · chain F against A, TM-score 0.99

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 P40011
Elsewhere: RCSB PDB 2C5Q · PDBe 2C5Q · UniProt P40011

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