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Crystal structure of S283A duck delta 2 crystallin mutant

Analyse Crystal structure of S283A duck delta 2 crystallin mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1K7W
Type: protein
Length: 1,795 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Delta 2 crystallin
EC: 4.3.2.1
UniProt: P24058
Ligands: AS1
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 69% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Delta 2 crystallin (EC 4.3.2.1)	protein	449	68% helix, 7% strand	P24058
B	Delta 2 crystallin (EC 4.3.2.1)	protein	448	69% helix, 7% strand	P24058
C	Delta 2 crystallin (EC 4.3.2.1)	protein	448	69% helix, 5% strand	P24058
D	Delta 2 crystallin (EC 4.3.2.1)	protein	450	68% helix, 5% strand	P24058

Ligands and binding sites

AS1 · Argininosuccinate · ligand · 4 copies · chains A, C, D, B

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	696	0.78	0.83	63	AS1
2	683	0.78	0.83	66	AS1
3	812	0.78	0.82	74	AS1
4	827	0.77	0.80	66	AS1
5	77	0.76	0.99	18	empty

Interfaces

6 interfaces between chains.

A–C · 3850 Å² buried · 67 hydrogen bonds · protein-protein
B–D · 3843 Å² buried · 73 hydrogen bonds · protein-protein
B–C · 1899 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 1886 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1756 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

1K7W · Crystal Structure of S283A Duck Delta 2 Crystallin Mutant · the same entry in another collection · chain D against D, TM-score 1.00
P24058 · AlphaFold monomer V2.0 prediction for argininosuccinate lyase (P24058) · a predicted model of the same protein · 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 P24058
Elsewhere: RCSB PDB 1K7W · PDBe 1K7W · UniProt P24058

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