1ND6: 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 2.4 Å resolution. Released 20 Dec 2002.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 12,048
Mol. weight: 169.63 kDa
Ligands: PO4, NAG, GLY
Released: 20 Dec 2002

Explore 1ND6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1ND6 contains 98 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: 26 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-11	10	1
β-strand	15	1	2
α-helix	28-30	3
β-strand	38	1	2
α-helix	40-56	17
α-helix	67-69	3
β-strand	70-75	6	1
α-helix	78-91	14
α-helix	96-98	3
β-strand	112-114	3	1
α-helix	116-118	3
α-helix	124	1
α-helix	126	1
α-helix	130-141	12
α-helix	143-149	7
α-helix	150-152	3
α-helix	153-163	11
α-helix	170-173	4
α-helix	174-178	5
α-helix	179-186	8
α-helix	189-192	4
α-helix	197-215	19
α-helix	220-226	7
α-helix	229-244	16
β-strand	251-256	6	1
α-helix	258-267	10
α-helix	275-277	3
β-strand	281-289	9	1
β-strand	292-300	9	1
α-helix	306-307	2
β-strand	308-309	2	1
α-helix	310	1
β-strand	313	1	3
β-strand	315	1	3
β-strand	318-320	3	1
α-helix	321-328	8
α-helix	329-331	3
α-helix	336-339	4

Chain B: 24 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	1001-1010	10	4
β-strand	1014	1	5
α-helix	1027-1029	3
β-strand	1037	1	5
α-helix	1039-1055	17
β-strand	1069-1074	6	4
α-helix	1077-1090	14
α-helix	1095-1097	3
β-strand	1111-1113	3	4
α-helix	1115-1117	3
α-helix	1123	1
α-helix	1125	1
α-helix	1129-1140	12
α-helix	1142-1148	7
α-helix	1149-1151	3
α-helix	1152-1162	11
α-helix	1169-1172	4
α-helix	1173-1177	5
α-helix	1178-1185	8
α-helix	1188-1191	4
α-helix	1196-1214	19
α-helix	1219-1225	7
α-helix	1227-1241	15
β-strand	1250-1255	6	4
α-helix	1257-1267	11
α-helix	1274-1276	3
β-strand	1280-1287	8	4
β-strand	1292-1299	8	4
α-helix	1305-1306	2
β-strand	1307-1309	3	4
β-strand	1318-1319	2	4
α-helix	1320-1327	8
α-helix	1328-1330	3
α-helix	1335-1338	4

Chain C: 24 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2001-2010	10	6
β-strand	2014	1	7
α-helix	2027-2029	3
β-strand	2037	1	7
α-helix	2039-2055	17
β-strand	2069-2074	6	6
α-helix	2077-2090	14
α-helix	2095-2097	3
β-strand	2111-2113	3	6
α-helix	2115-2117	3
α-helix	2123	1
α-helix	2125	1
α-helix	2129-2140	12
α-helix	2142-2148	7
α-helix	2149-2151	3
α-helix	2152-2155	4
α-helix	2158-2162	5
α-helix	2169-2172	4
α-helix	2173-2177	5
α-helix	2178-2185	8
α-helix	2188-2191	4
α-helix	2196-2214	19
α-helix	2219-2225	7
α-helix	2228-2243	16
β-strand	2250-2255	6	6
α-helix	2257-2267	11
β-strand	2280-2287	8	6
β-strand	2292-2299	8	6
α-helix	2305-2306	2
β-strand	2307-2309	3	6
β-strand	2312	1	8
β-strand	2314	1	8
β-strand	2318-2319	2	6
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
β-strand	3037	1	10
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	3129-3140	12
α-helix	3142-3148	7
α-helix	3149-3151	3
α-helix	3152-3162	11
α-helix	3169-3172	4
α-helix	3173-3177	5
α-helix	3178-3185	8
α-helix	3188-3191	4
α-helix	3196-3214	19
α-helix	3219-3225	7
α-helix	3227-3243	17
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	3335-3338	4

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

>1ND6_1 prostatic acid phosphatase (chains A, B, C, D)
KELKFVTLVFRHGDRSPIDTFPTDPIKESSWPQGFGQLTQLGMEQHYELGEYIRKRYRKF
LNESYKHEQVYIRSTDVDRTLMSAMTNLAALFPPEGVSIWNPILLWQPIPVHTVPLSEDQ
LLYLPFRNCPRFQELESETLKSEEFQKRLHPYKDFIATLGKLSGLHGQDLFGIWSKVYDP
LYCESVHNFTLPSWATEDTMTKLRELSELSLLSLYGIHKQKEKSRLQGGVLVNEILNHMK
RATQIPSYKKLIMYSAHDTTVSGLQMALDVYNGLLPPYASCHLTELYFEKGEYFVEMYYR
NETQHEPYPLMLPGCSPSCPLERFAELVGPVIPQDWSTECMTTNSHQGTEDSTD

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	4
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
GLY	Glycine	C2 H5 N O2	1

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
9YTD 2.5 Å, Designed antibody vAB66 targeting PAP-HLA A*02:01
1ND5 2.9 Å, Crystal Structures of Human Prostatic Acid Phosphatase in Complex with a Phosphate Ion…
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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