MolNFT v1 · #59443 · protein

Crystal structure of a transcriptional regulator from oenococcus oeni

3BY6 · Predicted transcriptional regulator: “Crystal structure of a transcriptional regulator from oenococcus oeni”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.58). MolNFT v1 #59443 on GenesisL1: 3D structure, binding…

PDB: 3BY6
Type: protein
Length: 602 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Predicted transcriptional regulator
UniProt: Q04D30
Ligands: CA
Pockets: 6 · best druggability 0.58

Structure

x-ray diffraction · 5 distinct chains · 60% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Predicted transcriptional regulator	protein	119	61% helix, 8% strand	Q04D30
B	Predicted transcriptional regulator	protein	118	61% helix, 8% strand	Q04D30
C	Predicted transcriptional regulator	protein	120	60% helix, 8% strand	Q04D30
D	Predicted transcriptional regulator	protein	121	60% helix, 8% strand	Q04D30
E	Predicted transcriptional regulator	protein	124	60% helix, 8% strand	Q04D30

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	449	0.58	0.74	35	empty
2	56	0.40	0.81	12	empty
3	139	0.39	0.74	27	empty
4	77	0.34	0.75	18	empty
5	73	0.32	0.75	22	empty

Interfaces

6 interfaces between chains.

A–D · 1929 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 366 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 365 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 323 Å² buried · 1 hydrogen bond · protein-protein
C–E · 268 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3BY6 · Crystal structure of a transcriptional regulator from Oenococcus oeni · 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 Q04D30
Elsewhere: RCSB PDB 3BY6 · PDBe 3BY6 · UniProt Q04D30

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