MolNFT v1 · #135929 · protein

Crystal structure of the coiled-coil domain from listeria innocua phage integrase (tetragonal form II)

5UDO · A118 serine integrase: “Crystal structure of the coiled-coil domain from listeria innocua phage integrase (tetragonal form II)”. X-ray diffraction, 5 pockets (best druggability 0.82). MolNFT v1 #135929 on GenesisL1: 3D structure…

PDB: 5UDO
Type: protein
Length: 374 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: A118 serine integrase
UniProt: Q928V6
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H	A118 serine integrase	protein	48	65% helix, 0% strand	Q928V6
B	A118 serine integrase	protein	49	73% helix, 0% strand	Q928V6
C	A118 serine integrase	protein	44	77% helix, 0% strand	Q928V6
D, F	A118 serine integrase	protein	48	85% helix, 0% strand	Q928V6
E	A118 serine integrase	protein	47	70% helix, 0% strand	Q928V6
G	A118 serine integrase	protein	42	76% helix, 0% strand	Q928V6

Pockets

5 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	977	0.82	0.84	95	empty
2	144	0.44	0.75	18	empty
3	106	0.41	0.77	16	empty
4	83	0.35	0.75	16	empty
5	67	0.34	0.76	13	empty

Interfaces

15 interfaces between chains.

G–H · 596 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 594 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 589 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 565 Å² buried · 7 hydrogen bonds · protein-protein
E–H · 548 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5UDO · Crystal structure of the coiled-coil domain from Listeria Innocua Phage Integrase… · 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 Q928V6
Elsewhere: RCSB PDB 5UDO · PDBe 5UDO · UniProt Q928V6

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