9F1I: Heavy chain rabbit fab

Crystal structure of a first-in-class antibody for alpha-1,6-fucosylated prostate-specific antigen, target bound. Determined by X-ray diffraction at 1.38 Å resolution. Released 31 Jul 2024.

Method: X-ray diffraction
Resolution: 1.38 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 6
Atoms: 7,511
Mol. weight: 97.05 kDa
Ligands: PFX
Released: 31 Jul 2024

Explore 9F1I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F1I contains 35 α-helices and 88 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: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	10-11	2	2
β-strand	17-24	8	1
β-strand	33-39	7	3
β-strand	45-52	8	3
β-strand	59-61	3	3
α-helix	63-65	3
β-strand	69-75	7	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	3
β-strand	111-114	4	3
β-strand	118-120	3	3
β-strand	121-122	2	2
α-helix	125-127	3
β-strand	128	1	4
α-helix	129-130	2
β-strand	131-135	5	5
α-helix	142-143	2
β-strand	146-156	11	5
β-strand	157	1	4
β-strand	162-165	4	6
α-helix	166-168	3
β-strand	170	1	6
β-strand	174-176	3	5
α-helix	177-179	3
β-strand	180-181	2	5
β-strand	187-196	10	5
β-strand	202-208	7	6
α-helix	209-211	3
β-strand	213-219	7	6

Chain I: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
β-strand	10-11	2	8
β-strand	17-24	8	7
β-strand	33-39	7	9
β-strand	45-52	8	9
β-strand	59-61	3	9
α-helix	63-65	3
β-strand	69-75	7	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-99	8	9
α-helix	100	1
β-strand	111-114	4	9
β-strand	118-120	3	9
β-strand	121-122	2	8
α-helix	126-127	2
β-strand	128	1	10
α-helix	129-130	2
β-strand	131-135	5	11
α-helix	142-143	2
β-strand	146-156	11	11
β-strand	157	1	10
β-strand	162-165	4	12
α-helix	166-168	3
β-strand	170	1	12
β-strand	174-176	3	11
α-helix	177-179	3
β-strand	180-181	2	11
β-strand	187-196	10	11
β-strand	203-208	6	12
α-helix	209-211	3
β-strand	213-218	6	12

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	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	84-93	10	14
β-strand	100-104	5	14
β-strand	108-113	6	14
β-strand	117	1	15
β-strand	120-124	5	16
α-helix	125-127	3
α-helix	131-133	3
β-strand	135-145	11	16
β-strand	146	1	15
β-strand	150-155	6	17
β-strand	158-159	2	17
α-helix	160	1
β-strand	164-168	5	16
α-helix	169-172	4
β-strand	178-187	10	16
α-helix	188-192	5
β-strand	196-203	8	17
β-strand	206-213	8	17
α-helix	214-216	3

Chain M: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	10-14	5	19
β-strand	19-25	7	18
β-strand	33-38	6	19
β-strand	45-49	5	19
β-strand	53-54	2	19
α-helix	55	1
β-strand	62-67	6	18
β-strand	70-75	6	18
α-helix	80-82	3
β-strand	84-93	10	19
β-strand	100-104	5	19
β-strand	108-113	6	19
β-strand	117	1	20
α-helix	118-119	2
β-strand	120-124	5	21
α-helix	125-127	3
α-helix	131-133	3
β-strand	135-145	11	21
β-strand	146	1	20
β-strand	150-155	6	22
β-strand	158-159	2	22
β-strand	164-168	5	21
α-helix	169-172	4
β-strand	178-187	10	21
α-helix	188-192	5
β-strand	196-203	8	22
β-strand	206-213	8	22
α-helix	214-216	3

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	68-74	7

Chain Q: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	68-75	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain rabbit fab	H, I	protein	230	Oryctolagus cuniculus
Light chain rabbit fab	L, M	protein	217	Oryctolagus cuniculus
Prostate specific antigen	P, Q	protein	10	Homo sapiens	P07288 (AlphaFold model)

Sequence of entity 1 (H, I), FASTA

>9F1I_1 Heavy chain rabbit fab (chains H, I)
QSLEESGGDLVKPGASLTLTCTASGFSFSAGYDMCWVRQAPGKGLEWIACIYADGSGSTY
YANWAKGRFTISLASSTTVTLQMTGLTAADTATYFCAREGADGPDYGYAAFSLWGPGTLV
TVSSGQPKAPSVFPLAPCCGDTPSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSV
RQSSGLYSLSSVVSVTSSSQPVTCNVAHPATNTKVDKTVAPSTCSKPTCP

Sequence of entity 2 (L, M), FASTA

>9F1I_2 Light chain rabbit fab (chains L, M)
DVVMTQTPASVEAAVGGTVTIKCQASQSISNYFSWYQQKPGQPPKLLIYKASTLASGVPS
RFKGSGSGTEFTLTISDLECADAATYYCQSFYGSVTSDYGGFAFGGGTEVVVKGDPVAPT
VLIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNL
SSTLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC

Sequence of entity 3 (P, Q), FASTA

>9F1I_3 Prostate specific antigen (chains P, Q)
IRNKSVILLG

Ligands and cofactors

ID	Name	Formula	Copies
PFX	2-[2-(2-azanylethoxy)ethoxy]ethanoic acid	C6 H13 N O4	2

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

Primary citation

Development of a first-in-class antibody and a specific assay for alpha-1,6-fucosylated prostate-specific antigen. Halldorsson, S., Hillringhaus, L., Hojer, C. et al. Sci Rep (2024) 14:16512-16512. DOI 10.1038/s41598-024-67545-1 · PubMed

Other PDB entries of the same protein (UniProt P07288 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9ZJQ 2.2 Å, Human KLK3 following acylation by CDD-3290
2ZCH 2.83 Å, Crystal structure of human prostate specific antigen complexed with an activating antibody
2ZCK 3.1 Å, Crystal structure of a ternary complex between PSA, a substrat-acyl intermediate and an…
3QUM 3.2 Å, Crystal structure of human prostate specific antigen (PSA) in Fab sandwich with a high…
2ZCL 3.25 Å, Crystal structure of human prostate specific antigen complexed with an activating antibody

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