3C2A: Antibody Fab fragment 447-52D

Antibody Fab fragment 447-52D in complex with UG1033 peptide. Determined by X-ray diffraction at 2.1 Å resolution. Released 8 Jul 2008.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 6
Atoms: 7,071
Mol. weight: 97.94 kDa
Released: 8 Jul 2008

Explore 3C2A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3C2A contains 33 α-helices and 100 β-strands across 6 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: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	11-12	2	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	45-51	7	10
α-helix	52B-53	3
β-strand	57-59	3	10
β-strand	67-72	6	8
α-helix	73-75	3
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-100A	14	10
β-strand	100F-103	10	10
β-strand	107-109	3	10
β-strand	110-111	2	9
β-strand	117	1	11
α-helix	118-119	2
β-strand	120-124	5	12
β-strand	137-147	11	12
β-strand	148	1	11
β-strand	153-157	4	13
α-helix	162-164	3
β-strand	166	1	13
β-strand	171-173	3	12
α-helix	174-176	3
β-strand	177-178	2	12
α-helix	179	1
β-strand	185-194	10	12
α-helix	195-197	3
β-strand	207-212	6	13
α-helix	213-215	3
β-strand	217-222	6	13

Chain I: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	21
β-strand	11-12	2	22
β-strand	18-25	8	21
α-helix	29-31	3
β-strand	34-39	6	23
β-strand	45-51	7	23
β-strand	57-59	3	23
β-strand	67-72	6	21
α-helix	73-75	3
β-strand	77-82	6	21
α-helix	84-86	3
β-strand	88-100A	14	23
β-strand	100F-103	10	23
β-strand	107-109	3	23
β-strand	110-111	2	22
β-strand	117	1	24
α-helix	118-119	2
β-strand	120-124	5	25
β-strand	137-147	11	25
β-strand	148	1	24
β-strand	153-157	4	13
α-helix	162-164	3
β-strand	166	1	13
β-strand	171-173	3	25
α-helix	174-176	3
β-strand	177-178	2	25
β-strand	185-194	10	25
α-helix	195-197	3
β-strand	207-212	6	13
α-helix	213-215	3
β-strand	217-222	6	13

Chain L: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	5	1	2
β-strand	9-13	4	3
β-strand	19-24	6	2
α-helix	27-29	5
β-strand	34-38	5	3
β-strand	45-48	4	3
β-strand	49	1	4
β-strand	53	1	4
α-helix	54-55	2
β-strand	62-67	6	2
β-strand	70-75	6	2
α-helix	80-82	3
β-strand	84-91	8	3
β-strand	96-98	3	3
β-strand	99	1	1
β-strand	102-106	5	3
β-strand	111	1	5
α-helix	112-113	2
β-strand	114-118	5	6
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	6
β-strand	140	1	5
β-strand	145-150	6	7
β-strand	153-155	3	7
β-strand	159-161	3	6
α-helix	162-164	3
β-strand	165-166	2	6
β-strand	173-181	9	6
α-helix	183-188	6
β-strand	192-198	7	7
β-strand	203-209	7	7
α-helix	211-213	3

Chain M: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	14
β-strand	5	1	15
β-strand	9-13	4	16
β-strand	19-24	6	15
α-helix	32-33	2
β-strand	34-38	5	16
β-strand	45-48	4	16
β-strand	49	1	17
β-strand	53	1	17
β-strand	62-67	6	15
β-strand	70-75	6	15
α-helix	80-82	3
β-strand	84-91	8	16
β-strand	96-98	3	16
β-strand	99	1	14
β-strand	102-106	5	16
β-strand	111	1	18
α-helix	112-113	2
β-strand	114-118	5	19
α-helix	122-126	5
β-strand	130-139	10	19
β-strand	140	1	18
β-strand	145-150	6	20
β-strand	154-155	2	20
β-strand	159-161	3	19
α-helix	162-164	3
β-strand	165-166	2	19
β-strand	173-181	9	19
α-helix	183-188	6
β-strand	192-198	7	20
β-strand	203-209	7	20

Chains P and Q: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	306-309	4	10
β-strand	318	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab 447-52D light chain	L, M	protein	216	Homo sapiens	P0DOY2 (AlphaFold model)
Fab 447-52D heavy chain	H, I	protein	231	Homo sapiens
Envelope glycoprotein	P, Q	protein	13	Human immunodeficiency virus 1	Q9YWB6

Sequence of entity 1 (L, M), FASTA

>3C2A_1 Fab 447-52D light chain (chains L, M)
QSVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVLWYQQFPGTAPKLLIYGNNKRPSGIP
DRFSGSKSGTSATLGITGLQTGDEADYFCATWDSGLSADWVFGGGTKLTVLSQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC

Sequence of entity 2 (H, I), FASTA

>3C2A_2 Fab 447-52D heavy chain (chains H, I)
EVQLVESGGGLVKPGGSLRLTCVASGFTFSDVWLNWVRQAPGKGLEWVGRIKSRTDGGTT
DYAASVKGRFTISRDDSKNTLYLQMNSLKTEDTAVYSCTTDGFIMIRGVSEDYYYYYMDV
WGKGTTVTVSSASTKGPSVFPLAPCSRSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVNHKPSNTKVDKRVEL

Sequence of entity 3 (P, Q), FASTA

>3C2A_3 Envelope glycoprotein (chains P, Q)
KSIHLGPGRAFYA

Primary citation

Structure determination of an anti-HIV-1 Fab 447-52D-peptide complex from an epitaxially twinned data set. Dhillon, A.K., Stanfield, R.L., Gorny, M.K. et al. Acta Crystallogr D Biol Crystallogr (2008) 64:792-802. DOI 10.1107/S0907444908013978 · PubMed

Other PDB entries of the same protein (UniProt P0DOY2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LLD 1.19 Å, Structure of wild-type IgG1 antibody heavy chain constant domain 1 and light chain…
3TV3 1.29 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with…
4LLQ 1.42 Å, Structure of redesigned IgG1 first constant and lambda domains (CH1:Clambda constant…
4LLY 1.6 Å, Crystal structure of Pertuzumab Clambda Fab with variable and constant domain redesigns…
3TWC 1.65 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT127 in complex with…
4LLM 1.75 Å, Structure of redesigned IgG1 first constant and lambda domains (CH1:Clambda constant…
8ECV 1.81 Å, Bovine Fab 2F12
1AQK 1.84 Å, Three-dimensional structure of a human FAB with high affinity for tetanus toxoid
1JVK 1.94 Å, Three-dimensional structure of an immunoglobulin light chain dimer acting as a lethal…
4LLW 1.95 Å, Crystal structure of Pertuzumab Clambda Fab with variable domain redesign (VRD2) at 1.95A
4EOW 1.97 Å, Crystal structure of a disease-associated anti-human GM-CSF autoantibody MB007
7FAB 2.0 Å, Crystal structure of human immunoglobulin fragment FAB new refined at 2.0 Å resolution

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