2B4J: Integrase

Structural basis for the recognition between HIV-1 integrase and LEDGF/p75. Determined by X-ray diffraction at 2.02 Å resolution. Released 25 Oct 2005.

Method: X-ray diffraction
Resolution: 2.02 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 4
Atoms: 3,757
Mol. weight: 59.52 kDa
Ligands: PO4
Released: 25 Oct 2005

Explore 2B4J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2B4J contains 25 α-helices and 10 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	60-68	9	1
β-strand	71-78	8	1
β-strand	83-89	7	1
α-helix	94-107	14
β-strand	112-114	3	1
α-helix	119-122	4
α-helix	124-133	10
β-strand	136-138	3	1
α-helix	151-165	15
α-helix	166-168	3
α-helix	172-185	14
α-helix	196-207	12

Chain B: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	60-68	9	2
β-strand	71-78	8	2
β-strand	83-89	7	2
α-helix	94-107	14
β-strand	112-115	4	2
α-helix	119-122	4
α-helix	124-133	10
α-helix	135	1
β-strand	136-139	4	2
α-helix	145-165	21
α-helix	166-168	3
α-helix	172-185	14
α-helix	196-207	12

Chain C: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	347-362	16
α-helix	370-381	12
α-helix	387-391	5
α-helix	394-403	10
α-helix	410-425	16

Chain D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	347-362	16
α-helix	370-382	13
α-helix	387-391	5
α-helix	394-403	10
α-helix	410-425	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrase (IN)	A, B	protein	166	Human immunodeficiency virus 1	P12497
PC4 and SFRS1 interacting protein	C, D	protein	98	Homo sapiens	O75475 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2B4J_1 Integrase (IN) (chains A, B)
GSHMHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAG
RWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKKIIGQVR
DQAEHLKTAVQMAVFIHNKKRKGGIGGYSAGERIVDIIATDIQTKE

Sequence of entity 2 (C, D), FASTA

>2B4J_2 PC4 and SFRS1 interacting protein (chains C, D)
GSSMDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIR
RFKVSQVIMEKSTMLYNKFKNMFLVGEGDSVITQVLNK

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75. Cherepanov, P., Ambrosio, A.L., Rahman, S. et al. Proc Natl Acad Sci U S A (2005) 102:17308-17313. DOI 10.1073/pnas.0506924102 · PubMed

Other PDB entries of the same protein (UniProt P12497), best resolution first:

3DS4 1.12 Å, HIV-1 capsid C-terminal domain mutant (L211S) in complex with an inhibitor of particle…
3DS2 1.2 Å, HIV-1 capsid C-terminal domain mutant (Y169A)
6T6E 1.3 Å, Crystal Structure of the C-terminal domain of the HIV-1 Integrase (PNL4-3)
2XDE 1.4 Å, Crystal structure of the complex of PF-3450074 with an engineered HIV capsid N terminal…
3L3U 1.4 Å, Crystal structure of the HIV-1 integrase core domain to 1.4A
2PWO 1.45 Å, Crystal Structure of HIV-1 CA146 A92E Psuedo Cell
3WNF 1.45 Å, Cyclic hexapeptide CKIDNC in complex with HIV-1 integrase
6OYD 1.46 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-004
6MCR 1.48 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-001
2PXR 1.5 Å, Crystal Structure of HIV-1 CA146 in the Presence of CAP-1
3WNH 1.5 Å, Cyclic hexapeptide PKZDNv in complex with HIV-1 integrase
4NX4 1.5 Å, Re-refinement of CAP-1 HIV-CA complex

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