MolNFT v1 · #188985 · protein + DNA

Higher-order assembly of multiple mmtv strand transfer complex intasomes

7UT1 · Integrase: “Higher-order assembly of multiple mmtv strand transfer complex intasomes”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.83). MolNFT v1 #188985 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7UT1
Type: protein + DNA
Length: 3,445 residues
Chains: 28
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrase; Vdna strand (non-transferred); Vdna-tdna strand (transferred); Tdna strand
UniProt: O56220
Ligands: ZN
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 19 distinct chains · 39% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a, e, A	Integrase	protein	264	42% helix, 17% strand	O56220
b	Integrase	protein	244	41% helix, 21% strand	O56220
c, C	Integrase	protein	48	6% helix, 50% strand	O56220
d, D	Integrase	protein	49	6% helix, 43% strand	O56220
f	Integrase	protein	243	39% helix, 22% strand	O56220
g	Integrase	protein	236	41% helix, 23% strand	O56220
h	Integrase	protein	231	39% helix, 23% strand	O56220
i, l, I, L	Vdna strand (non-transferred)	dna	22	—	—
j, J	Vdna-tdna strand (transferred)	dna	40	—	—
k, K	Tdna strand	dna	14	—	—
m	Vdna-tdna strand (transferred)	dna	38	—	—
n	Tdna strand	dna	12	—	—
B	Integrase	protein	242	39% helix, 21% strand	O56220
E	Integrase	protein	265	42% helix, 18% strand	O56220
F	Integrase	protein	235	42% helix, 22% strand	O56220
G	Integrase	protein	235	42% helix, 25% strand	O56220
H	Integrase	protein	230	42% helix, 23% strand	O56220
M	Vdna-tdna strand (transferred)	dna	39	—	—
N	Tdna strand	dna	13	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains a, b, e, f, g, h, A, B, E, F, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	726	0.83	0.87	78	empty
2	646	0.82	0.87	65	empty
3	776	0.80	0.84	61	empty
4	786	0.79	0.83	61	empty
5	920	0.76	0.79	59	empty

Interfaces

81 interfaces between chains.

e–f · 2079 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 2030 Å² buried · 10 hydrogen bonds · protein-protein
a–b · 1984 Å² buried · 10 hydrogen bonds · protein-protein
g–h · 1966 Å² buried · 11 hydrogen bonds · protein-protein
G–H · 1952 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

7UT1 · Higher-order assembly of multiple MMTV strand transfer complex intasomes · the same entry in another collection · chain F against F, 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 O56220
Elsewhere: RCSB PDB 7UT1 · PDBe 7UT1 · UniProt O56220

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