MolNFT v1 · #63432 · protein

Two domain fragment of HIV-2 integrase in complex with ledgf ibd

3F9K: “Two domain fragment of HIV-2 integrase in complex with ledgf ibd”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.86). MolNFT v1 #63432 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3F9K
Type: protein
Length: 5,928 residues
Chains: 36
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrase; PC4 and SFRS1-interacting protein
UniProt: P04584, O75475
Ligands: ZN, MG
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I, M, Q, U, Y, c, g, k, o, s	Integrase	protein	204	45% helix, 17% strand	P04584
B, F, J, N, R, V, Z, d, h, l, p, t	Integrase	protein	196	49% helix, 17% strand	P04584
C, G, K, O, S, W, a, e, i, m, q, u	PC4 and SFRS1-interacting protein	protein	94	71% helix, 4% strand	O75475

Ligands and binding sites

ZN · Zinc ion · metal · 24 copies · chains A, B, E, F, I, J, M, N, Q, R, U, V, Y, Z, c, d, g, h, k, l, o, p, s, t
MG · Magnesium ion · metal · 24 copies · chains A, B, E, F, I, J, M, N, Q, R, U, V, Y, Z, c, d, g, h, k, l, o, p, s, t

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	917	0.86	0.87	137	empty
2	638	0.83	0.87	81	empty
3	568	0.82	0.87	80	empty
4	581	0.82	0.87	74	empty
5	447	0.82	0.89	45	empty

Interfaces

101 interfaces between chains.

I–J · 1539 Å² buried · 28 hydrogen bonds · protein-protein
s–t · 1537 Å² buried · 28 hydrogen bonds · protein-protein
Y–Z · 1537 Å² buried · 28 hydrogen bonds · protein-protein
U–V · 1536 Å² buried · 26 hydrogen bonds · protein-protein
M–N · 1535 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

3F9K · Two domain fragment of HIV-2 integrase in complex with LEDGF IBD · 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 P04584
Every structure of UniProt O75475
Elsewhere: RCSB PDB 3F9K · PDBe 3F9K · UniProt P04584 · UniProt O75475

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