4RRP: Fab

Crystal Structure of the Fab complexed with antigen Asf1p, Northeast Structural Genomics Consortium (NESG) Target PdR16. Determined by X-ray diffraction at 2.79 Å resolution. Released 31 Dec 2014.

Method: X-ray diffraction
Resolution: 2.79 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae
Chains: 18
Atoms: 27,161
Mol. weight: 402.46 kDa
Released: 31 Dec 2014

Explore 4RRP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4RRP contains 120 α-helices and 329 β-strands across 18 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: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	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	70-75	6	1
α-helix	80-82	3
β-strand	85-90	6	2
β-strand	93	1	3
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-154	2	6
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-186	4
β-strand	191-197	7	6
β-strand	205-210	6	6

Chain B: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	85-90	6	14
β-strand	93	1	15
α-helix	96	1
β-strand	97-98	2	14
β-strand	102-106	5	14
α-helix	107	1
β-strand	111	1	16
α-helix	112-113	2
β-strand	114-118	5	17
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	17
β-strand	140	1	16
β-strand	145-150	6	18
β-strand	153-154	2	18
α-helix	155	1
β-strand	159-163	5	17
α-helix	164-167	4
β-strand	173-182	10	17
α-helix	183-187	5
β-strand	191-197	7	18
β-strand	205-210	6	18

Chain C: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	10-13	4	25
β-strand	19-25	7	24
β-strand	33-38	6	25
β-strand	45-49	5	25
β-strand	53-54	2	25
α-helix	55	1
β-strand	62-67	6	24
β-strand	70-75	6	24
α-helix	80-82	3
β-strand	85-90	6	25
β-strand	93	1	26
β-strand	97-98	2	25
β-strand	102-106	5	25
β-strand	111	1	27
β-strand	114-118	5	28
α-helix	122-126	5
β-strand	129-139	11	28
β-strand	140	1	27
β-strand	145-150	6	29
β-strand	153-154	2	29
β-strand	159-163	5	28
α-helix	164-167	4
β-strand	173-182	10	28
α-helix	183-186	4
β-strand	191-198	8	29
β-strand	201-210	10	29

Chain D: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	35
β-strand	10-13	4	36
β-strand	19-25	7	35
β-strand	33-38	6	36
β-strand	45-49	5	36
β-strand	53-54	2	36
α-helix	55	1
β-strand	62-67	6	35
β-strand	70-75	6	35
α-helix	80-82	3
β-strand	85-90	6	36
β-strand	93	1	37
β-strand	97-98	2	36
β-strand	102-106	5	36
β-strand	111	1	38
α-helix	112-113	2
β-strand	114-118	5	39
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	39
β-strand	140	1	38
β-strand	144-150	7	40
β-strand	153-154	2	40
α-helix	155	1
β-strand	159-163	5	39
α-helix	164-167	4
β-strand	173-182	10	39
α-helix	183-186	4
β-strand	191-198	8	40
β-strand	205-210	6	40

Chain E: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	46
β-strand	10-13	4	47
β-strand	19-25	7	46
β-strand	33-38	6	47
β-strand	45-49	5	47
β-strand	53-54	2	47
α-helix	55	1
β-strand	62-67	6	46
β-strand	70-75	6	46
α-helix	80-82	3
β-strand	85-90	6	47
β-strand	93	1	48
α-helix	96	1
β-strand	97-98	2	47
β-strand	102-106	5	47
α-helix	107	1
β-strand	111	1	49
β-strand	114-118	5	50
α-helix	119-121	3
β-strand	129-139	11	50
β-strand	140	1	49
β-strand	144-150	7	51
β-strand	153-155	3	51
β-strand	159-160	2	50
β-strand	163	1	50
α-helix	165-167	3
β-strand	173-182	10	50
α-helix	183-186	4
β-strand	191-198	8	51
β-strand	205-210	6	51

Chain F: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	57
β-strand	10-13	4	58
β-strand	19-25	7	57
β-strand	34-38	5	58
α-helix	43-44	2
β-strand	45-48	4	58
β-strand	54	1	58
β-strand	62-67	6	57
β-strand	70-75	6	57
β-strand	85-89	5	58
β-strand	93	1	59
α-helix	96	1
β-strand	98	1	58
β-strand	102-106	5	58
β-strand	111	1	60
β-strand	114-115	2	61
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-137	9	61
β-strand	140	1	60
β-strand	147-150	4	62
β-strand	154	1	62
β-strand	163	1	61
α-helix	165-167	3
β-strand	175-182	8	61
α-helix	183-186	4
β-strand	191-196	6	62
β-strand	205-210	6	62
β-strand	211	1	63
β-strand	213	1	63

Chain G: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	46-51	6	8
β-strand	57-59	3	8
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-95	8	8
β-strand	102-103	2	8
β-strand	107-111	5	8
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
β-strand	132	1	11
β-strand	135	1	11
β-strand	136-145	10	10
β-strand	146	1	9
β-strand	151-154	4	12
α-helix	155-157	3
β-strand	159	1	12
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-184	9	10
α-helix	186-188	3
β-strand	195-200	6	12
α-helix	201-203	3
β-strand	205-210	6	12
α-helix	213-215	3

Chain H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	10-12	3	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	33-39	7	20
β-strand	46-51	6	20
β-strand	57-59	3	20
β-strand	67-72	6	19
β-strand	77-82	6	19
α-helix	84-86	3
β-strand	88-95	8	20
β-strand	102-103	2	20
β-strand	108-111	4	20
α-helix	115-116	2
β-strand	117	1	21
α-helix	118-119	2
β-strand	120-124	5	22
α-helix	125-127	3
β-strand	135-145	11	22
β-strand	146	1	21
β-strand	151-154	4	23
α-helix	155-157	3
β-strand	159	1	23
β-strand	163-165	3	22
β-strand	169-170	2	22
β-strand	176-185	10	22
α-helix	186-188	3
β-strand	195-200	6	23
β-strand	205-210	6	23

10 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 antibody, light chain	A, B, C, D, E, F	protein	216	Homo sapiens	Q7Z3Y4 (AlphaFold model)
Fab antibody, heavy chain	G, H, I, J, K, L	protein	238	Homo sapiens	P01857 (AlphaFold model)
Antigen Asf1p	M, N, O, P, Q, R	protein	160	Saccharomyces cerevisiae	P32447 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>4RRP_1 Fab antibody, light chain (chains A, B, C, D, E, F)
MSDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGV
PSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSQWYPITFGQGTKVEIKRTVAAPSVFIF
PPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (G, H, I, J, K, L), FASTA

>4RRP_2 Fab antibody, heavy chain (chains G, H, I, J, K, L)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVSYSSIHWVRQAPGKGLEWVAYIYPSSGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSYSTKLAMDYWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTSRHHHHHH

Sequence of entity 3 (M, N, O, P, Q, R), FASTA

>4RRP_3 Antigen Asf1p (chains M, N, O, P, Q, R)
GSSIVSLLGIKVLNNPAKFTDPYEFEITFECLESLKHDLEWKLTYVGSSRSLDHDQELDS
ILVGPVPVGVNKFVFSADPPSAELIPASELVSVTVILLSCSYDGREFVRVGYYVNNEYDE
EELRENPPAKVQVDHIVRNILAEKPRVTRFNIVWDNENEG

Primary citation

Crystal Structure of the Fab complexed with antigen Asf1p, Northeast Structural Genomics Consortium (NESG) Target PdR16. Kuzin, A., Lew, S., Seetharaman, J. et al. To be published.

Other PDB entries of the same protein (UniProt Q7Z3Y4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VSI 1.51 Å, CH1/Ckappa Fab mutant 15.1
6MY4 1.69 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M,LC-S30bR]
6MY5 1.73 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M,LC-S30bR]
4PUB 1.75 Å, Crystal structure of Fab DX-2930
1L7I 1.8 Å, Crystal Structure of the anti-ErbB2 Fab2C4
6MXS 1.95 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M]
6MXR 2.04 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M]
4OGY 2.1 Å, Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 Angstrom…
5VR9 2.15 Å, CH1/Ckappa Fab based on Matuzumab
9MY8 2.3 Å, D7 Herpes Virus Simplex Neutralizing Nanobody Bound to HSV Glycoprotein gD
4OGX 2.4 Å, Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.4 Angstrom…
8CWJ 2.45 Å, Fab arms of antibodies 4C12-B12 and CR3022 bound to pangolin receptor binding domain…

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