2OQJ: Crystal structure analysis of Fab 2G12

Crystal structure analysis of Fab 2G12 in complex with peptide 2G12.1. Determined by X-ray diffraction at 2.8 Å resolution. Released 15 Jan 2008.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 12
Atoms: 13,685
Mol. weight: 195.98 kDa
Released: 15 Jan 2008

Explore 2OQJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2OQJ contains 59 α-helices and 183 β-strands across 12 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: 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
α-helix	43-44	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	85-92	8	2
β-strand	95-98	4	2
β-strand	102-106	5	2
β-strand	111	1	3
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	183-187	5
β-strand	191-198	8	5
β-strand	205-210	6	5

Chain B: 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
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	195-197	3
β-strand	206-212	7	10
α-helix	213-215	3
β-strand	217-225	7	10

Chains C and I: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	11
β-strand	14-16	3	11

Chain D: 9 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
α-helix	43-44	2
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	85-92	8	13
β-strand	95-98	4	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	183-187	5
β-strand	191-198	8	16
β-strand	205-210	6	16

Chain E: 9 helices, 22 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	137-147	11	20
β-strand	148	1	19
β-strand	153-157	4	21
α-helix	162-164	3
β-strand	166	1	21
β-strand	171-173	3	20
α-helix	174-176	3
β-strand	177-178	2	20
β-strand	185-194	10	20
α-helix	195-199	5
β-strand	206-212	7	21
α-helix	213-215	3
β-strand	217-225	7	21

Chains F and L: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	22
β-strand	14-17	4	22

Chain G: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	23
β-strand	10-13	4	24
β-strand	18-25	8	23
β-strand	33-38	6	24
β-strand	45-49	5	24
β-strand	53-54	2	24
α-helix	55	1
β-strand	56	1	25
β-strand	58	1	25
β-strand	62-67	6	23
β-strand	70-76	7	23
α-helix	80-82	3
β-strand	85-92	8	24
β-strand	95-98	4	24
β-strand	102-106	5	24
β-strand	111	1	26
α-helix	112-113	2
β-strand	114-118	5	27
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	27
β-strand	140	1	26
β-strand	144-150	7	28
β-strand	153-154	2	28
β-strand	159-163	5	27
α-helix	164-167	4
β-strand	173-182	10	27
α-helix	183-186	4
β-strand	191-198	8	28
β-strand	205-210	6	28

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	29
β-strand	11-13	3	30
β-strand	18-25	8	29
α-helix	29-31	3
β-strand	34-39	6	31
β-strand	45-51	7	31
α-helix	52A-54	3
β-strand	57-59	3	31
β-strand	67-72	6	29
β-strand	77-82	6	29
α-helix	84-86	3
β-strand	88-95	8	31
β-strand	100F-103	4	31
β-strand	107-109	3	31
β-strand	110-112	3	30
β-strand	117	1	32
α-helix	118-119	2
β-strand	120-124	5	33
β-strand	137-147	11	33
β-strand	148	1	32
β-strand	153-157	4	34
α-helix	162-164	3
β-strand	166	1	34
β-strand	171-173	3	33
α-helix	174-176	3
β-strand	177-178	2	33
β-strand	185-194	10	33
α-helix	195-197	3
β-strand	206-212	7	34
α-helix	213-215	3
β-strand	217-225	7	34

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab 2G12 light chain	A, D, G, J	protein	211	Homo sapiens	Q6PIH4
Fab 2G12 heavy chain	B, E, H, K	protein	224	Homo sapiens	Q6N089 (AlphaFold model)
peptide 2G12.1 (ACPPSHVLDMRSGTCLAAEGK)	C, F, I, L	protein	21

Sequence of entity 1 (A, D, G, J), FASTA

>2OQJ_1 Fab 2G12 light chain (chains A, D, G, J)
VVMTQSPSTLSASVGDTITITCRASQSIETWLAWYQQKPGKAPKLLIYKASTLKTGVPSR
FSGSGSGTEFTLTISGLQFDDFATYHCQHYAGYSATFGQGTRVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Sequence of entity 2 (B, E, H, K), FASTA

>2OQJ_2 Fab 2G12 heavy chain (chains B, E, H, K)
EVQLVESGGGLVKAGGSLILSCGVSNFRISAHTMNWVRRVPGGGLEWVASISTSSTYRDY
ADAVKGRFTVSRDDLEDFVYLQMHKMRVEDTAIYYCARKGSDRLSDNDPFDAWGPGTVVT
VSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 3 (C, F, I, L), FASTA

>2OQJ_3 peptide 2G12.1 (ACPPSHVLDMRSGTCLAAEGK) (chains C, F, I, L)
ACPPSHVLDMRSGTCLAAEGK

Primary citation

A peptide inhibitor of HIV-1 neutralizing antibody 2G12 is not a structural mimic of the natural carbohydrate epitope on gp120. Menendez, A., Calarese, D.A., Stanfield, R.L. et al. FASEB J (2008) 22:1380-1392. DOI 10.1096/fj.07-8983com · PubMed

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