6N2X: Anti-HIV-1 Fab 2G12 + Man9 re-refinement

Anti-HIV-1 Fab 2G12 + Man9 re-refinement. Determined by X-ray diffraction at 3.0 Å resolution. Released 28 Nov 2018.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,835
Mol. weight: 97.95 kDa
Released: 28 Nov 2018

Explore 6N2X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N2X contains 32 α-helices and 88 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: 8 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
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
α-helix	125-127	3
β-strand	138-147	10	9
β-strand	148	1	8
β-strand	153-157	4	10
α-helix	162-164	3
β-strand	171-173	3	9
α-helix	174-176	3
β-strand	177-178	2	9
β-strand	185-193	9	9
α-helix	195-197	3
β-strand	198	1	11
β-strand	203	1	11
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	12
β-strand	10-13	4	13
β-strand	18-25	8	12
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-76	7	12
α-helix	80-82	3
β-strand	85-91	7	13
β-strand	96-98	3	13
β-strand	102-106	5	13
β-strand	111	1	14
α-helix	112-113	2
β-strand	114-118	5	15
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	15
β-strand	140	1	14
β-strand	144-150	7	16
β-strand	153-154	2	16
α-helix	155	1
β-strand	159-163	5	15
α-helix	164-167	4
β-strand	173-182	10	15
α-helix	183-186	4
β-strand	191-198	8	16
β-strand	205-210	6	16

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	122-126	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
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, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	10-13	4	18
β-strand	18-25	8	17
α-helix	29-31	3
β-strand	34-39	6	18
β-strand	45-51	7	18
α-helix	52A-54	3
β-strand	57-59	3	18
β-strand	67-72	6	17
β-strand	77-82	6	17
α-helix	84-86	3
β-strand	88-95	8	18
β-strand	100F-103	4	18
β-strand	107-112	6	18
β-strand	117	1	19
α-helix	118-119	2
β-strand	120-124	5	20
α-helix	125-127	3
β-strand	138-147	10	20
β-strand	148	1	19
β-strand	153-157	4	21
α-helix	162-164	3
β-strand	171-173	3	20
α-helix	174-176	3
β-strand	177-178	2	20
β-strand	185-193	9	20
α-helix	195-197	3
β-strand	198	1	22
β-strand	203	1	22
β-strand	207-212	6	21
β-strand	217-222	6	21

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	P0DOX5 (AlphaFold model)

Sequence of entity 1 (K, L), FASTA

>6N2X_1 Fab 2G12 light chain (chains K, L)
DVVMTQSPSTLSASVGDTITITCRASQSIETWLAWYQQKPGKAPKLLIYKASTLKTGVPS
RFSGSGSGTEFTLTISGLQFDDFATYHCQHYAGYSATFGQGTRVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 2 (H, M), FASTA

>6N2X_2 Fab 2G12 heavy chain (chains H, M)
EVQLVESGGGLVKAGGSLILSCGVSNFRISAHTMNWVRRVPGGGLEWVASISTSSTYRDY
ADAVKGRFTVSRDDLEDFVYLQMHKMRVEDTAIYYCARKGSDRLSDNDPFDAWGPGTVVT
VSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

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
6N35 1.75 Å, Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement
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

Browse structure collections

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