3QUM: Prostate-specific antigen

Crystal structure of human prostate specific antigen (PSA) in Fab sandwich with a high affinity and a PCa selective antibody. Determined by X-ray diffraction at 3.2 Å resolution. Released 9 Nov 2011.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Homo sapiens, Mus musculus
Chains: 10
Atoms: 17,606
Mol. weight: 249.84 kDa
Released: 9 Nov 2011

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

Secondary structure: helices and β-sheets

3QUM contains 41 α-helices and 204 β-strands across 10 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: 2 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	15
β-strand	12-14	3	16
β-strand	19-22	4	15
β-strand	27C-27D	2	17
β-strand	30-31	2	17
β-strand	33-38	6	18
β-strand	45-49	5	18
β-strand	62-66	5	15
β-strand	71-75	5	15
β-strand	84-90	7	18
β-strand	97-98	2	18
β-strand	102-104	3	18
β-strand	105-107	3	16
β-strand	115-118	4	19
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-137	8	19
β-strand	145-150	6	20
β-strand	153	1	20
β-strand	159-163	5	19
β-strand	174-181	8	19
β-strand	191-198	8	20
β-strand	201-210	10	20

Chain B: 1 helix, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	21
α-helix	6-9	4
β-strand	10-11	2	22
β-strand	19-20	2	23
β-strand	23	1	23
β-strand	25	1	21
β-strand	33-39	7	24
β-strand	46-51	6	24
β-strand	57-59	3	24
β-strand	67-72	6	23
β-strand	77-82	6	23
β-strand	89-95	7	24
β-strand	97	1	25
β-strand	99	1	25
β-strand	103-104	2	24
β-strand	108-109	2	24
β-strand	110-111	2	22
β-strand	122-125	4	26
β-strand	136-137	2	27
β-strand	140-144	5	26
β-strand	154-155	2	28
β-strand	171	1	29
β-strand	176	1	29
β-strand	177-181	5	26
β-strand	184-185	2	27
β-strand	196-197	2	28
β-strand	200	1	30
β-strand	205	1	30

Chain C: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	47
β-strand	14	1	48
β-strand	19-24	6	47
β-strand	27D	1	49
β-strand	30	1	49
β-strand	33-38	6	50
β-strand	45-49	5	50
β-strand	62-66	5	47
β-strand	70-75	6	47
β-strand	84-90	7	50
β-strand	97-98	2	50
β-strand	102-104	3	50
β-strand	107	1	48
β-strand	114-118	5	51
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	51
β-strand	146-150	5	52
β-strand	153-155	3	52
β-strand	159-163	5	51
α-helix	164-166	3
β-strand	173-182	10	51
α-helix	183-186	4
β-strand	191-196	6	52
β-strand	205-210	6	52

Chain D: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	53
α-helix	7-9	3
β-strand	10	1	54
β-strand	18-23	6	53
β-strand	33-38	6	54
β-strand	46-51	6	54
β-strand	57-59	3	54
β-strand	68-72	5	53
β-strand	77-82	6	53
α-helix	84-86	3
β-strand	88-95	8	54
β-strand	103-104	2	54
β-strand	108-110	3	54
β-strand	122-125	4	55
β-strand	136-144	9	55
β-strand	153-155	3	56
α-helix	156-158	3
β-strand	164-172	9	55
β-strand	175-185	11	55
β-strand	196-200	5	56
α-helix	201-203	3
β-strand	205-209	5	56

Chain H: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	9
β-strand	10-12	3	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	46-52	7	10
β-strand	56-59	4	10
α-helix	61-63	3
β-strand	67-72	6	9
α-helix	73-75	3
β-strand	77-82	6	9
α-helix	84-86	3
β-strand	88-94	7	10
β-strand	102-103	2	10
β-strand	107-111	5	10
β-strand	117	1	11
β-strand	121-122	2	12
β-strand	136-138	3	13
β-strand	141-145	5	12
β-strand	146	1	11
β-strand	151-154	4	14
α-helix	155-157	3
β-strand	163-165	3	13
β-strand	169	1	12
β-strand	175-178	4	12
β-strand	179-183	5	13
β-strand	194-199	6	14
α-helix	200-202	3
β-strand	204-209	6	14

Chain K: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	42
β-strand	10-12	3	43
β-strand	19-25	7	42
β-strand	34-39	6	43
β-strand	46-49	4	43
β-strand	51-52	2	44
β-strand	56-57	2	44
β-strand	67-72	6	42
β-strand	77-82	6	42
α-helix	84-86	3
β-strand	88-94	7	43
β-strand	102-103	2	43
β-strand	107-111	5	43
α-helix	118-120	3
β-strand	121-124	4	45
β-strand	136-145	10	45
β-strand	151-154	4	46
α-helix	155-157	3
β-strand	164-165	2	45
β-strand	169-170	2	45
β-strand	175-183	9	45
α-helix	185-187	3
β-strand	194-199	6	46
β-strand	204-209	6	46

Chain L: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4	1	4
β-strand	10-13	4	5
β-strand	19-24	6	6
β-strand	25	1	4
β-strand	33-38	6	5
β-strand	45-49	5	5
β-strand	53-54	2	5
β-strand	62-67	6	6
β-strand	70-75	6	6
β-strand	84-90	7	5
β-strand	97-98	2	5
β-strand	102-106	5	5
β-strand	116-118	3	7
α-helix	122-125	4
β-strand	129-136	8	7
β-strand	147-149	3	8
β-strand	159-163	5	7
α-helix	164-166	3
β-strand	175-182	8	7
α-helix	183-187	5
β-strand	192-195	4	8
β-strand	206-209	4	8

Chain M: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	36
β-strand	10-13	4	37
β-strand	19-24	6	36
β-strand	33-38	6	37
β-strand	45-46	2	37
β-strand	48-49	2	38
β-strand	53-54	2	38
α-helix	55	1
β-strand	62-65	4	36
β-strand	70-75	6	36
α-helix	80-82	3
β-strand	84-90	7	37
β-strand	97-98	2	37
β-strand	102-106	5	37
α-helix	112-113	2
β-strand	114-118	5	39
α-helix	122-126	5
β-strand	129-131	3	40
β-strand	133-139	7	39
β-strand	144-149	6	41
β-strand	161-163	3	39
β-strand	173-177	5	39
β-strand	180-182	3	40
α-helix	183-187	5
β-strand	192-198	7	41
β-strand	201-209	9	41

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
Prostate-specific antigen	P, Q	protein	237	Homo sapiens	P07288 (AlphaFold model)
Fab 5D3D11 Light Chain	L, M	protein	219	Mus musculus
Fab 5D3D11 Heavy Chain	H, K	protein	219	Mus musculus
Fab 5D5A5 Light Chain	A, C	protein	218	Mus musculus
Fab 5D5A5 Heavy Chain	B, D	protein	219	Mus musculus

Sequence of entity 1 (P, Q), FASTA

>3QUM_1 Prostate-specific antigen (chains P, Q)
IVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPE
DTGQVFQVSHSFPHPLYDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTDAVKVMDLPTQ
EPALGTTCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVTKFMLCAGRWTG
GKSTCSGDSGGPLVCNGVLQGITSWGSEPCALPERPSLYTKVVHYRKWIKDTIVANP

Sequence of entity 2 (L, M), FASTA

>3QUM_2 Fab 5D3D11 Light Chain (chains L, M)
DIVMTQTAPSVFVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLA
SGVPDRFSGSGSGTDFTLRISRVEAEDVGVYYCMQHLEYPVTFGAGTKVEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (H, K), FASTA

>3QUM_3 Fab 5D3D11 Heavy Chain (chains H, K)
QVQLQQSGPELVKPGASVKISCKVSGYAISSSWMNWVKQRPGQGLEWIGRIYPGDGDTKY
NGKFKDKATLTVDKSSSTAYMQLSSLTSVDSAVYFCARDGYRYYFDYWGQGTSVTVSSAK
TTAPPVYPLAPVCGDTTGSSVTLGCLVKGYFPESVTLLWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIVPRD

Sequence of entity 4 (A, C), FASTA

>3QUM_4 Fab 5D5A5 Light Chain (chains A, C)
DIVLTQSPPSLAVSLGQRATISCRASESIDLYGFTFMHWYQQKPGQPPKILIYRASNLES
GIPARFSGSGSRTDFTLTINPVEADDVATYYCQQTHEDPYTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 5 (B, D), FASTA

>3QUM_5 Fab 5D5A5 Heavy Chain (chains B, D)
QVQLQQSGAELAKPGASVKMSCKTSGYSFSSYWMHWVKQRPGQGLEWIGYINPSTGYTEN
NQKFKDKVTLTADKSSNTAYMQLNSLTSEDSAVYYCARSGRLYFDVWGAGTTVTVSSAKT
TAPPVYPLAPVCGDTTGSSVTLGCLVKGYFPESVTLLWNSGSLSSGVHTFPAVLQSDLYT
LSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIVPRDC

Primary citation

Crystal structure of human prostate-specific antigen in a sandwich antibody complex. Stura, E.A., Muller, B.H., Bossus, M. et al. J Mol Biol (2011) 414:530-544. DOI 10.1016/j.jmb.2011.10.007 · PubMed

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

9F1I 1.38 Å, Crystal structure of a first-in-class antibody for alpha-1,6-fucosylated…
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…
2ZCL 3.25 Å, Crystal structure of human prostate specific antigen complexed with an activating antibody

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