6MUB: Anti-HIV-1 Fab 2G12 + Man5 re-refinement

Anti-HIV-1 Fab 2G12 + Man5 re-refinement. Determined by X-ray diffraction at 2.5 Å resolution. Released 31 Oct 2018.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,705
Mol. weight: 96.22 kDa
Released: 31 Oct 2018

Explore 6MUB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MUB contains 28 α-helices and 86 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 H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-13	4	7
β-strand	18-25	8	6
β-strand	33-39	7	7
β-strand	45-51	7	7
α-helix	52A-54	3
β-strand	57-59	3	7
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-95	8	7
β-strand	100F-103	4	7
β-strand	107-112	6	7
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	9
β-strand	133-134	2	9
β-strand	137-147	11	9
β-strand	148	1	8
β-strand	153-157	4	10
α-helix	162-164	3
β-strand	166	1	10
β-strand	171-173	3	9
α-helix	174-176	3
β-strand	177-178	2	9
β-strand	185-194	10	9
α-helix	195-198	4
β-strand	207-212	6	10
α-helix	213-215	3
β-strand	217-222	6	10

Chain K: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-13	4	12
β-strand	18-25	8	11
β-strand	34-38	5	12
β-strand	45-49	5	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-67	6	11
β-strand	70-76	7	11
α-helix	80-82	3
β-strand	85-91	7	12
β-strand	96-98	3	12
β-strand	102-106	5	12
β-strand	111	1	13
α-helix	112-113	2
β-strand	114-118	5	14
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	14
β-strand	140	1	13
β-strand	145-150	6	15
β-strand	153-154	2	15
α-helix	155	1
β-strand	159-163	5	14
β-strand	173-182	10	14
α-helix	183-187	5
β-strand	191-197	7	15
β-strand	205-210	6	15

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	18-25	8	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-76	7	1
α-helix	80-82	3
β-strand	85-91	7	2
β-strand	96-98	3	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	144-150	7	5
β-strand	153-154	2	5
α-helix	155	1
β-strand	159-163	5	4
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	191-198	8	5
β-strand	205-210	6	5

Chain M: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
β-strand	10-13	4	17
β-strand	18-25	8	16
β-strand	34-39	6	17
β-strand	45-51	7	17
α-helix	52A-54	3
β-strand	57-59	3	17
β-strand	67-72	6	16
β-strand	77-82	6	16
α-helix	84-86	3
β-strand	88-95	8	17
β-strand	100F-103	4	17
β-strand	107-112	6	17
β-strand	117	1	18
α-helix	118-119	2
β-strand	120-124	5	19
β-strand	137-147	11	19
β-strand	148	1	18
β-strand	153-157	4	20
α-helix	162-164	3
β-strand	171-173	3	19
α-helix	174-176	3
β-strand	177-178	2	19
β-strand	185-194	10	19
α-helix	195-198	4
β-strand	207-212	6	20
α-helix	213-215	3
β-strand	217-222	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab 2G12, light chain	K, L	protein	213	Homo sapiens	P0DOX7 (AlphaFold model)
Fab 2G12, heavy chain	H, M	protein	226	Homo sapiens	P0DOX5 (AlphaFold model)

Sequence of entity 1 (K, L), FASTA

>6MUB_1 Fab 2G12, light chain (chains K, L)
DVVMTQSPSTLSASVGDTITITCRASQSIETWLAWYQQKPGKAPKLLIYKASTLKTGVPS
RFSGSGSGTEFTLTISGLQFDDFATYHCQHYAGYSATFGQGTRVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 2 (H, M), FASTA

>6MUB_2 Fab 2G12, heavy chain (chains H, M)
EVQLVESGGGLVKAGGSLILSCGVSNFRISAHTMNWVRRVPGGGLEWVASISTSSTYRDY
ADAVKGRFTVSRDDLEDFVYLQMHKMRVEDTAIYYCARKGSDRLSDNDPFDAWGPGTVVT
VSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Primary citation

Dissection of the carbohydrate specificity of the broadly neutralizing anti-HIV-1 antibody 2G12. Calarese, D.A., Lee, H.K., Huang, C.Y. et al. Proc Natl Acad Sci U S A (2005) 102:13372-13377. DOI 10.1073/pnas.0505763102 · PubMed

Other PDB entries of the same protein (UniProt P0DOX7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6UOE 1.8 Å, 3-25 Fab germline-reversion variant bound to an HCMV gB-derived peptide
6MSY 2.0 Å, Anti-HIV-1 Fab Fab 2G12 + Man4 re-refinement
6MU3 2.33 Å, Anti-HIV-1 Fab 2G12 + Man7 re-refinement
8BBO 2.75 Å, SARS-CoV-2 Delta-RBD complexed with BA.2-36 Fab
2R56 2.8 Å, Crystal Structure of a Recombinant IgE Fab Fragment in Complex with Bovine…
6UTE 2.9 Å, Crystal structure of Z032 Fab in complex with WNV EDIII
5VIC 3.0 Å, Crystal structure of anti-Zika antibody Z004 bound to DENV-1 Envelope protein DIII
5VIG 3.0 Å, Crystal structure of anti-Zika antibody Z006 bound to Zika virus envelope protein DIII
6UTA 3.1 Å, Crystal structure of Z004 iGL Fab in complex with ZIKV EDIII
2QAD 3.3 Å, Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4
4XI5 3.9 Å, gHgL of varicella-zoster virus in complex with human neutralizing antibodies
6NQD 3.9 Å, Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab

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