Research workbench

Obody NL8 bound to hen egg-white lysozyme

Analyse Obody NL8 bound to hen egg-white lysozyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GLA
Type: protein
Length: 436 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysozyme C; Obody NL8
EC: 3.2.1.17
UniProt: P00698
Pockets: 6 · best druggability 0.36

Structure

x-ray diffraction · 3 distinct chains · 21% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lysozyme C (EC 3.2.1.17)	protein	129	41% helix, 11% strand	P00698
C	Obody NL8	protein	89	7% helix, 52% strand	—
D	Obody NL8	protein	89	8% helix, 53% strand	—

Pockets

6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	120	0.36	0.73	27	empty
2	76	0.33	0.74	18	empty
3	58	0.31	0.76	15	empty
4	79	0.31	0.73	22	empty
5	66	0.31	0.74	16	empty

Interfaces

3 interfaces between chains.

A–D · 869 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 841 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 664 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4GLA · OBody NL8 bound to hen egg-white lysozyme · the same entry in another collection · chain B against B, 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 P00698
Elsewhere: RCSB PDB 4GLA · PDBe 4GLA · UniProt P00698

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