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Co-crystal structure of LIF1P-LIG4P

Analyse Co-crystal structure of LIF1P-LIG4P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1Z56
Type: protein
Length: 557 residues
Chains: 11
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ligase interacting factor 1; DNA ligase IV
EC: 6.5.1.1
UniProt: P53150, Q08387
Pockets: 9 · best druggability 0.75

Structure

x-ray diffraction · 10 distinct chains · 31% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ligase interacting factor 1	protein	77	66% helix, 0% strand	P53150
B	Ligase interacting factor 1	protein	76	76% helix, 0% strand	P53150
C	DNA ligase IV (EC 6.5.1.1)	protein	237	25% helix, 8% strand	Q08387
D	Ligase interacting factor 1	protein	8	0% helix, 38% strand	—
E, H	Ligase interacting factor 1	protein	7	0% helix, 43% strand	—
F	Ligase interacting factor 1	protein	45	0% helix, 11% strand	—
G	Ligase interacting factor 1	protein	37	0% helix, 5% strand	—
I	Ligase interacting factor 1	protein	30	0% helix, 3% strand	—
J	Ligase interacting factor 1	protein	20	0% helix, 0% strand	—
K	Ligase interacting factor 1	protein	13	0% helix, 8% strand	—

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	706	0.75	0.80	93	empty
2	406	0.68	0.80	42	empty
3	798	0.67	0.74	80	empty
4	57	0.59	0.91	20	empty
5	220	0.49	0.75	26	empty

Interfaces

20 interfaces between chains.

A–B · 1430 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 1006 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 835 Å² buried · 3 hydrogen bonds · protein-protein
F–G · 365 Å² buried · 5 hydrogen bonds · protein-protein
I–K · 277 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1Z56 · Co-Crystal Structure of Lif1p-Lig4p · the same entry in another collection · chain K against K, TM-score 1.00
P53150 · AlphaFold monomer V2.0 prediction for ligase-interacting factor 1 (P53150) · a predicted model of the same protein · chain A against A, TM-score 0.84

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 P53150
Every structure of UniProt Q08387
Elsewhere: RCSB PDB 1Z56 · PDBe 1Z56 · UniProt P53150 · UniProt Q08387

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