MolNFT v1 · #76415 · protein

Crystal structure of human beta-crystallin B3

3QK3: “Crystal structure of human beta-crystallin B3”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.88). MolNFT v1 #76415 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3QK3
Type: protein
Length: 527 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-crystallin B3
UniProt: P26998
Ligands: SO4
Pockets: 3 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-crystallin B3	protein	175	10% helix, 42% strand	P26998
B, C	Beta-crystallin B3	protein	176	9% helix, 44% strand	P26998

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · 5 copies · chains A, B

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

Pockets

3 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	1145	0.88	0.89	114	SO4
2	109	0.45	0.79	22	empty
3	101	0.42	0.77	18	empty

Interfaces

3 interfaces between chains.

A–B · 763 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 697 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 515 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3QK3 · Crystal structure of human beta-crystallin B3 · the same entry in another collection · chain A against A, TM-score 1.00
P26998 · AlphaFold monomer V2.0 prediction for beta-crystallin B3 (P26998) · a predicted model of the same protein · chain B 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 P26998
Elsewhere: RCSB PDB 3QK3 · PDBe 3QK3 · UniProt P26998

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