6L4B: Human WT NDRG3

Crystal structure of human WT NDRG3. Determined by X-ray diffraction at 2.2 Å resolution. Released 26 Aug 2020.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 6
Atoms: 13,453
Mol. weight: 248.7 kDa
Released: 26 Aug 2020

Explore 6L4B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6L4B contains 119 α-helices and 54 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 A: 19 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	31-37	7	1
β-strand	40-47	8	1
α-helix	55	1
β-strand	56-60	5	1
α-helix	67	1
α-helix	68-72	5
α-helix	73-75	3
α-helix	78-84	7
β-strand	89-93	5	1
α-helix	94	1
α-helix	101-105	5
α-helix	110-112	3
α-helix	113-118	6
α-helix	120-126	7
β-strand	132-137	6	1
α-helix	139-150	12
β-strand	155-161	7	1
α-helix	185-193	9
α-helix	196-201	6
α-helix	204-215	12
α-helix	219-230	12
α-helix	232-234	3
β-strand	237	1	2
β-strand	250	1	2
β-strand	255-261	7	1
α-helix	267-275	9
β-strand	282-287	6	1
α-helix	294-297	4
α-helix	299-312	14

Chain B: 22 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	30-36	7	3
β-strand	41-47	7	3
α-helix	55	1
β-strand	56-60	5	3
α-helix	67	1
α-helix	68-72	5
α-helix	73-75	3
α-helix	78-84	7
β-strand	89-93	5	3
α-helix	94	1
α-helix	101-105	5
α-helix	110-112	3
α-helix	113-117	5
α-helix	120-126	7
β-strand	132-137	6	3
α-helix	139-150	12
β-strand	155-161	7	3
α-helix	185-193	9
α-helix	196-201	6
α-helix	204-211	8
α-helix	212-216	5
α-helix	219-230	12
α-helix	232-234	3
α-helix	239-241	3
β-strand	255-261	7	3
α-helix	267-276	10
α-helix	279-281	3
β-strand	282-287	6	3
α-helix	294-297	4
α-helix	299-312	14

Chain C: 19 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	30-37	8	7
β-strand	40-47	8	7
β-strand	56-60	5	7
α-helix	67-76	10
α-helix	78-80	3
α-helix	81-84	4
β-strand	89-93	5	7
α-helix	94	1
α-helix	101-105	5
α-helix	110-112	3
α-helix	113-117	5
α-helix	120-126	7
β-strand	132-137	6	7
α-helix	139-150	12
α-helix	152-154	3
β-strand	155-161	7	7
α-helix	185-193	9
α-helix	196-201	6
α-helix	204-211	8
α-helix	212-216	5
α-helix	219-231	13
β-strand	237	1	8
α-helix	239-241	3
β-strand	250	1	8
β-strand	255-261	7	7
α-helix	267-275	9
β-strand	282-287	6	7
α-helix	294-297	4
α-helix	299-312	14

Chain D: 21 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	30-37	8	9
β-strand	40-47	8	9
α-helix	55	1
β-strand	56-60	5	9
α-helix	67	1
α-helix	68-72	5
α-helix	73-75	3
α-helix	78-84	7
β-strand	89-93	5	9
α-helix	94	1
α-helix	101-105	5
α-helix	110-112	3
α-helix	113-118	6
α-helix	120-126	7
β-strand	132-137	6	9
α-helix	139-150	12
β-strand	155-161	7	9
α-helix	185-193	9
α-helix	196-201	6
α-helix	203-215	13
α-helix	219-230	12
α-helix	232-234	3
α-helix	239-241	3
β-strand	255-261	7	9
α-helix	267-275	9
α-helix	279-281	3
β-strand	282-287	6	9
α-helix	294-297	4
α-helix	299-312	14

Chain E: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	31-37	7	4
β-strand	40-47	8	4
β-strand	56-60	5	4
α-helix	67-75	9
α-helix	78-81	4
β-strand	89-93	5	4
α-helix	94	1
α-helix	101-105	5
α-helix	110-112	3
α-helix	113-117	5
α-helix	120-126	7
β-strand	132-137	6	4
α-helix	139-150	12
β-strand	155-161	7	4
α-helix	185-193	9
α-helix	196-201	6
α-helix	203-215	13
α-helix	219-230	12
α-helix	232-234	3
β-strand	237	1	5
α-helix	239-241	3
β-strand	250	1	5
β-strand	255-261	7	4
α-helix	267-275	9
β-strand	282-287	6	4
α-helix	294-297	4
α-helix	299-312	14

Chain F: 21 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	30-35	6	6
β-strand	42-47	6	6
β-strand	56-60	5	6
α-helix	61-62	2
α-helix	67	1
α-helix	68-72	5
α-helix	73-75	3
α-helix	81-84	4
β-strand	89-93	5	6
α-helix	94	1
α-helix	101-105	5
α-helix	110-112	3
α-helix	113-118	6
α-helix	120-126	7
β-strand	132-137	6	6
α-helix	139-150	12
β-strand	155-161	7	6
α-helix	185-193	9
α-helix	196-200	5
α-helix	203-215	13
α-helix	219-230	12
α-helix	232-234	3
α-helix	239-241	3
α-helix	246-248	3
β-strand	255-261	7	6
α-helix	267-275	9
β-strand	282-287	6	6
α-helix	294-297	4
α-helix	299-312	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein NDRG3	A, B, C, D, E, F	protein	375	Homo sapiens	Q9UGV2 (AlphaFold model)

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

>6L4B_1 Protein NDRG3 (chains A, B, C, D, E, F)
MDELQDVQLTEIKPLLNDKNGTRNFQDFDCQEHDIETTHGVVHVTIRGLPKGNRPVILTY
HDIGLNHKSCFNAFFNFEDMQEITQHFAVCHVDAPGQQEGAPSFPTGYQYPTMDELAEML
PPVLTHLSLKSIIGIGVGAGAYILSRFALNHPELVEGLVLINVDPCAKGWIDWAASKLSG
LTTNVVDIILAHHFGQEELQANLDLIQTYRMHIAQDINQDNLQLFLNSYNGRRDLEIERP
ILGQNDNKSKTLKCSTLLVVGDNSPAVEAVVECNSRLNPINTTLLKMADCGGLPQVVQPG
KLTEAFKYFLQGMGYIPSASMTRLARSRTHSTSSSLGSGESPFSRSVTSNQSDGTQESCE
SPDVLDRHQTMEVSC

Primary citation

Structural and Biophysical Analyses of Human N-Myc Downstream-Regulated Gene 3 (NDRG3) Protein. Kim, K.R., Kim, K.A., Park, J.S. et al. Biomolecules (2020) 10. DOI 10.3390/biom10010090 · PubMed

Other PDB entries of the same protein (UniProt Q9UGV2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9KCL 2.9 Å, Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 in (2Na+)E1-AMPPCP…
9KCM 2.9 Å, Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 and TMX2 in…
9KCR 3.2 Å, Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 in (2Na+)E1 state
6L4G 3.3 Å, Crystal structure of human NDRG3 I171M/S176H mutant
6L4H 3.4 Å, Crystal structure of human NDRG3 C30S mutant

Browse structure collections

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