5FA2: 426c.TM4deltaV1-3 p120

Crystal structure of 426c.TM4deltaV1-3 p120. Determined by X-ray diffraction at 2.0 Å resolution. Released 6 Apr 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Human immunodeficiency virus 1
Chains: 2
Atoms: 5,860
Mol. weight: 84 kDa
Ligands: NAG, FLC, SCN
Released: 6 Apr 2016

Explore 5FA2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5FA2 contains 22 α-helices and 54 β-strands across 2 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: 11 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	53-56	4	1
α-helix	65-73	9
β-strand	75-76	2	1
α-helix	77	1
β-strand	84-85	2	2
α-helix	86	1
β-strand	91-94	4	3
α-helix	99-115	17
β-strand	120-123	4	4
β-strand	199-202	4	4
β-strand	215	1	5
β-strand	216-218	3	1
β-strand	223-228	6	2
β-strand	236-239	4	3
β-strand	242-245	4	2
β-strand	247	1	1
α-helix	248-250	3
β-strand	251	1	5
β-strand	256	1	6
β-strand	259-261	3	6
α-helix	264-266	3
β-strand	271-273	3	6
β-strand	284-298	15	6
β-strand	328-334	7	6
α-helix	335-350	16
β-strand	357-360	4	6
α-helix	368-371	4
β-strand	373-377	5	6
β-strand	380-384	5	6
β-strand	413-421	9	6
β-strand	423-425	3	4
β-strand	432-434	3	4
α-helix	436-439	4
β-strand	443-456	14	6
α-helix	457-458	2
β-strand	465-470	6	6
α-helix	475-483	9
β-strand	486-490	5	2

Chain B: 11 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	53-56	4	7
α-helix	65-73	9
β-strand	75-76	2	7
α-helix	77	1
β-strand	84-85	2	8
α-helix	86	1
β-strand	91-94	4	9
α-helix	99-115	17
β-strand	120-122	3	10
β-strand	200-202	3	10
β-strand	215	1	11
β-strand	216-218	3	7
β-strand	223-228	6	8
β-strand	236-239	4	9
β-strand	242-245	4	8
β-strand	247	1	7
α-helix	248-250	3
β-strand	251	1	11
β-strand	256	1	12
β-strand	259-261	3	12
α-helix	264-266	3
β-strand	271-273	3	12
β-strand	284-298	15	12
β-strand	328-334	7	12
α-helix	335-350	16
β-strand	357-360	4	12
α-helix	368-371	4
β-strand	373-377	5	12
β-strand	380-384	5	12
β-strand	413-421	9	12
β-strand	423-425	3	10
β-strand	432-434	3	10
α-helix	436-439	4
β-strand	443-456	14	12
α-helix	457-458	2
β-strand	465-470	6	12
α-helix	476-483	8
β-strand	486-490	5	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
gp120	A, B	protein	353	Human immunodeficiency virus 1	M4Q8P8

Sequence of entity 1 (A, B), FASTA

>5FA2_1 gp120 (chains A, B)
VWKEAKTTLFCASDAKAYEKECHNVWATHACVPTDPNPQEVVLEQVTENFNMWKNDMVDQ
MQEDVISIWDQCLKPCVKLTNTSTLTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGK
GPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLRDNAKIIIVQLQKSVEIVC
TRPNNGGSGSGGDIRQAYCQISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITT
HSFNCGGEFFYCNTSGLFQDTISNATIMLPCRIKQIINMWQEVGKAIYAPPIKGQITCKS
DITGLLLLRDGGDTTDNTEIFRPSGGDMRDNWRSELYKYKVVEIKPLHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	11
FLC	Citrate anion	C6 H5 O7	4
SCN	Thiocyanate ion	C N S	1

Primary citation

Structural basis for germline antibody recognition of HIV-1 immunogens. Scharf, L., West, A.P., Sievers, S.A. et al. Elife (2016) 5. DOI 10.7554/eLife.13783 · PubMed

Other PDB entries of the same protein (UniProt M4Q8P8), best resolution first:

6MFT 2.31 Å, Crystal structure of glycosylated 426c HIV-1 gp120 core G459C in complex with glVRC01…
6P8M 3.59 Å, Crystal Structure of Antibody P-p3b3 A60C Heavy Chain in Complex with 426c HIV-1 gp120…
6MYY 3.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs…
6MZJ 4.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 Fabs…

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