1ND5: Human Prostatic Acid Phosphatase

Crystal Structures of Human Prostatic Acid Phosphatase in Complex with a Phosphate Ion and alpha-Benzylaminobenzylphosphonic Acid Update the Mechanistic Picture and Offer New Insights into Inhibitor Design. Determined by X-ray diffraction at 2.9 Å resolution. Released 20 Dec 2002.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,727
Mol. weight: 169.94 kDa
Ligands: NAG, NDG, 2BF
Released: 20 Dec 2002

Explore 1ND5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1ND5 contains 87 α-helices and 44 β-strands across 4 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: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-11	10	1
β-strand	15	1	2
α-helix	28-30	3
β-strand	32	1	3
β-strand	34	1	3
β-strand	38	1	2
α-helix	40-56	17
β-strand	70-74	5	1
α-helix	78-91	14
α-helix	96-98	3
β-strand	112	1	1
α-helix	116-118	3
α-helix	124	1
α-helix	126	1
α-helix	130-141	12
α-helix	143-163	21
α-helix	170-173	4
α-helix	174-178	5
α-helix	179-186	8
α-helix	197-215	19
α-helix	220-226	7
α-helix	229-244	16
β-strand	251-256	6	1
α-helix	258-268	11
β-strand	281-288	8	1
β-strand	293-300	8	1
α-helix	306-307	2
β-strand	308-310	3	1
β-strand	313	1	4
β-strand	315	1	4
β-strand	319-320	2	1
α-helix	321-328	8
α-helix	329-331	3
α-helix	336-340	5

Chain B: 22 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	1001-1010	10	5
β-strand	1014	1	6
α-helix	1027-1029	3
β-strand	1037	1	6
α-helix	1039-1055	17
β-strand	1069-1074	6	5
α-helix	1077-1090	14
β-strand	1111-1113	3	5
α-helix	1115-1117	3
α-helix	1123	1
α-helix	1125	1
α-helix	1132-1139	8
α-helix	1141-1147	7
α-helix	1148-1150	3
α-helix	1151-1161	11
α-helix	1168-1171	4
α-helix	1172-1176	5
α-helix	1177-1184	8
α-helix	1187-1190	4
α-helix	1195-1213	19
α-helix	1218-1224	7
α-helix	1226-1242	17
β-strand	1249-1254	6	5
α-helix	1256-1266	11
α-helix	1273-1275	3
β-strand	1279-1286	8	5
β-strand	1291-1298	8	5
β-strand	1306-1308	3	5
β-strand	1316-1318	3	5
α-helix	1319-1326	8
α-helix	1327-1329	3
α-helix	1334-1337	4

Chain C: 21 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2001-2010	10	7
β-strand	2014	1	8
α-helix	2027-2029	3
β-strand	2037	1	8
α-helix	2039-2055	17
β-strand	2069-2074	6	7
α-helix	2077-2090	14
β-strand	2111-2113	3	7
α-helix	2115-2117	3
α-helix	2123	1
α-helix	2125	1
α-helix	2129-2139	11
α-helix	2142-2148	7
α-helix	2149-2151	3
α-helix	2152-2162	11
α-helix	2169-2172	4
α-helix	2173-2177	5
α-helix	2178-2185	8
α-helix	2196-2214	19
α-helix	2219-2224	6
α-helix	2227-2243	17
β-strand	2250-2255	6	7
α-helix	2257-2267	11
β-strand	2280-2287	8	7
β-strand	2292-2299	8	7
α-helix	2305-2306	2
β-strand	2307-2309	3	7
β-strand	2318-2319	2	7
α-helix	2320-2327	8
α-helix	2328-2330	3
α-helix	2335-2338	4

Chain D: 24 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3001-3010	10	9
β-strand	3014	1	10
α-helix	3027-3029	3
α-helix	3036	1
β-strand	3037	1	10
α-helix	3038	1
α-helix	3039-3055	17
β-strand	3069-3074	6	9
α-helix	3077-3090	14
α-helix	3095-3097	3
β-strand	3111-3113	3	9
α-helix	3115-3117	3
α-helix	3123	1
α-helix	3125	1
α-helix	3129-3139	11
α-helix	3142-3148	7
α-helix	3153-3162	10
α-helix	3169-3171	3
α-helix	3172-3177	6
α-helix	3178-3185	8
α-helix	3196-3214	19
α-helix	3219-3225	7
α-helix	3227-3242	16
β-strand	3250-3255	6	9
α-helix	3257-3267	11
α-helix	3274-3276	3
β-strand	3280-3287	8	9
β-strand	3292-3299	8	9
α-helix	3305-3306	2
β-strand	3307-3309	3	9
β-strand	3318-3319	2	9
α-helix	3320-3327	8
α-helix	3328-3330	3
α-helix	3335-3339	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
prostatic acid phosphatase	A, B, C, D	protein	354	Homo sapiens	P15309 (AlphaFold model)

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

>1ND5_1 prostatic acid phosphatase (chains A, B, C, D)
KELKFVTLVFRHGDRSPIDTFPTDPIKESSWPQGFGQLTQLGMEQHYELGEYIRKRYRKF
LNESYKHEQVYIRSTDVDRTLMSAMTNLAALFPPEGVSIWNPILLWQPIPVHTVPLSEDQ
LLYLPFRNCPRFQELESETLKSEEFQKRLHPYKDFIATLGKLSGLHGQDLFGIWSKVYDP
LYCESVHNFTLPSWATEDTMTKLRELSELSLLSLYGIHKQKEKSRLQGGVLVNEILNHMK
RATQIPSYKKLIMYSAHDTTVSGLQMALDVYNGLLPPYASCHLTELYFEKGEYFVEMYYR
NETQHEPYPLMLPGCSPSCPLERFAELVGPVIPQDWSTECMTTNSHQGTEDSTD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
NDG	2-acetamido-2-deoxy-alpha-D-glucopyranose	C8 H15 N O6	1
2BF	Alpha-benzyl-aminobenzyl-phosphonic acid	C14 H16 N O3 P	4

Water and common crystallization additives (1PE) are not listed.

Primary citation

Crystal structures of human prostatic acid phosphatase in complex with a phosphate ion and alpha-benzylaminobenzylphosphonic acid update the mechanistic picture and offer new insights into inhibitor design. Ortlund, E., LaCount, M.W., Lebioda, L. Biochemistry (2003) 42:383-389. DOI 10.1021/bi0265067 · PubMed

Other PDB entries of the same protein (UniProt P15309 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3PPD 1.5 Å, GGVLVN segment from Human Prostatic Acid Phosphatase Residues 260-265, involved in…
9NMV 1.97 Å, TCR156 S32Halpha bound to HLA A*02:01-PAP
9NMY 2.01 Å, TCR156 S32Qalpha bound to HLA A*02:01-PAP
9NMU 2.1 Å, TCR156 bound to HLA A*02:01-PAP
9NMW 2.11 Å, TCR156 S30Ealpha S32Qalpha bound to HLA A*02:01-PAP
9NMX 2.19 Å, TCR156 S32Malpha variant bound to HLA A*02:01-PAP
1ND6 2.4 Å, Crystal Structures of Human Prostatic Acid Phosphatase in Complex with a Phosphate Ion…
9YTD 2.5 Å, Designed antibody vAB66 targeting PAP-HLA A*02:01
2HPA 2.9 Å, Structural origins of L(+)-tartrate inhibition of human prostatic acid phosphatase
8XJ4 3.19 Å, Structure of prostatic acid phosphatase in human semen
1CVI 3.2 Å, Crystal structure of human prostatic acid phosphatase
2L3H NMR Structure in a Membrane Environment Reveals Putative Amyloidogenic Regions of the…

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