6N35: Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement

Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement. Determined by X-ray diffraction at 1.75 Å resolution. Released 28 Nov 2018.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,150
Mol. weight: 94.92 kDa
Ligands: MAN, BEZ
Released: 28 Nov 2018

Explore 6N35 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N35 contains 31 α-helices and 85 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, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-13	4	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	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	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	206-212	7	10
β-strand	217-225	7	10

Chain K: 8 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	33-38	6	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
α-helix	164-167	4
β-strand	173-182	10	14
α-helix	183-186	4
β-strand	191-197	7	15
β-strand	205-210	6	15

Chain L: 8 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	122-127	6
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
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	191-198	8	5
β-strand	205-210	6	5

Chain M: 8 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
α-helix	29-31	3
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	206-212	7	20
α-helix	213-215	3
β-strand	217-225	7	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab 2G12 light chain	K, L	protein	213	Homo sapiens	P01834 (AlphaFold model)
Fab 2G12 heavy chain	H, M	protein	224	Homo sapiens	P01857 (AlphaFold model)

Sequence of entity 1 (K, L), FASTA

>6N35_1 Fab 2G12 light chain (chains K, L)
DVVMTQSPSTLSASVGDTITITCRASQSIETWLAWYQQKPGKAPKLLIYKASTLKTGVPS
RFSGSGSGTEFTLTISGLQFDDFATYHCQHYAGYSATFGQGTRVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 2 (H, M), FASTA

>6N35_2 Fab 2G12 heavy chain (chains H, M)
EVQLVESGGGLVKAGGSLILSCGVSNFRISAHTMNWVRRVPGGGLEWVASISTSSTYRDY
ADAVKGRFTVSRDDLEDFVYLQMHKMRVEDTAIYYCARKGSDRLSDNDPFDAWGPGTVVT
VSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Ligands and cofactors

ID	Name	Formula	Copies
MAN	alpha-D-mannopyranose	C6 H12 O6	1
BEZ	Benzoic acid	C7 H6 O2	1

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

Primary citation

Antibody domain exchange is an immunological solution to carbohydrate cluster recognition. Calarese, D.A., Scanlan, C.N., Zwick, M.B. et al. Science (2003) 300:2065-2071. DOI 10.1126/science.1083182 · PubMed

Other PDB entries of the same protein (UniProt P01834 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EWI 1.6 Å, Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing…
1NGZ 1.6 Å, Chimeric Germline Fab 7g12-apo
4XMP 1.78 Å, Crystal structure of broadly and potently neutralizing antibody VRC08 in complex with…
1N0X 1.8 Å, Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a…
3VH8 1.8 Å, KIR3DL1 in complex with HLA-B*5701
3X12 1.8 Å, Crystal structure of HLA-B*57:01.I80N
6B9Z 1.82 Å, Trastuzumab Fab v3
2VXQ 1.9 Å, Crystal structure of the major grass pollen allergen Phl p 2 in complex with its…
3D85 1.9 Å, Crystal structure of IL-23 in complex with neutralizing FAB
6BAH 1.9 Å, Trastuzumab Fab v3 with 5-diphenyl meditope variant
6DCV 1.9 Å, Crystal structure of human anti-tau antibody CBTAU-27.1
1GAF 1.95 Å, 48G7 hybridoma line FAB complexed with hapten 5-(para-nitrophenyl phosphonate)-pentanoic…

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