1K5D: Ran-GPPNHP-RanBP1-RanGAP complex

Crystal structure of Ran-GPPNHP-RanBP1-RanGAP complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 13 Feb 2002.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Homo sapiens, Schizosaccharomyces pombe
Chains: 12
Atoms: 22,738
Mol. weight: 366.51 kDa
Ligands: MG, GNP
Released: 13 Feb 2002

Explore 1K5D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1K5D contains 120 α-helices and 116 β-strands across 12 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.

Chains A, D and G: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	9-17	9	1
α-helix	23-32	10
β-strand	45-54	10	1
β-strand	57-66	10	1
α-helix	71	1
α-helix	74-76	3
α-helix	77-80	4
β-strand	85-91	7	1
α-helix	95-99	5
α-helix	101-112	12
β-strand	117-122	6	1
α-helix	138-141	4
β-strand	145-148	4	1
α-helix	159-169	11
β-strand	176	1	1
α-helix	182-185	4
α-helix	196-205	10

Chains B, E, H and K: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	49-58	10	2
β-strand	67-79	13	2
β-strand	86-92	7	2
β-strand	98-103	6	2
β-strand	112	1	2
β-strand	119-127	9	2
β-strand	134-141	8	2
α-helix	145-165	21

Chains C, I and L: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	3
β-strand	12-13	2	4
α-helix	19-22	4
α-helix	23-25	3
α-helix	26-30	5
β-strand	36-38	3	3
β-strand	43-44	2	4
α-helix	46-56	11
β-strand	64-66	3	3
α-helix	79-90	12
β-strand	98-100	3	3
α-helix	108-110	3
α-helix	111-120	10
β-strand	126-128	3	3
α-helix	136-154	19
α-helix	158-161	4
β-strand	163-165	3	3
α-helix	173-175	3
α-helix	176-185	10
β-strand	191-193	3	3
α-helix	201-206	6
α-helix	207-211	5
α-helix	212-214	3
β-strand	220-222	3	3
α-helix	229-239	11
α-helix	240-242	3
β-strand	248-250	3	3
α-helix	258-270	13
β-strand	278-280	3	3
β-strand	287	1	5
α-helix	288-301	14
β-strand	307-309	3	3
β-strand	314	1	5
α-helix	320-332	13

Chain F: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	8
β-strand	12-13	2	9
α-helix	19-22	4
α-helix	23-25	3
α-helix	26-30	5
β-strand	36-38	3	8
β-strand	43-44	2	9
α-helix	46-56	11
β-strand	64-66	3	8
α-helix	79-91	13
β-strand	98-100	3	8
α-helix	108-110	3
α-helix	111-120	10
β-strand	126-128	3	8
α-helix	136-154	19
α-helix	158-161	4
β-strand	163-165	3	8
α-helix	173-175	3
α-helix	176-185	10
β-strand	191-193	3	8
α-helix	201-206	6
α-helix	207-211	5
α-helix	212-214	3
β-strand	220-222	3	8
α-helix	229-239	11
α-helix	240-242	3
β-strand	248-250	3	8
α-helix	258-270	13
β-strand	278-280	3	8
β-strand	287	1	10
α-helix	288-301	14
β-strand	307-309	3	8
β-strand	314	1	10
α-helix	320-332	13

Chain J: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	9-17	9	16
α-helix	23-32	10
β-strand	45-54	10	16
β-strand	57-66	10	16
α-helix	71	1
α-helix	74-76	3
α-helix	77-80	4
β-strand	85-91	7	16
α-helix	95-99	5
α-helix	101-112	12
β-strand	117-122	6	16
α-helix	138-142	5
β-strand	145-148	4	16
α-helix	159-169	11
β-strand	176	1	16
α-helix	182-185	4
α-helix	196-205	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTP-binding nuclear protein RAN	A, D, G, J	protein	216	Homo sapiens	P62826 (AlphaFold model)
Ran-specific GTPase-activating protein	B, E, H, K	protein	201	Homo sapiens	P43487 (AlphaFold model)
Ran GTPase activating protein 1	C, F, I, L	protein	386	Schizosaccharomyces pombe	P41391 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>1K5D_1 GTP-binding nuclear protein RAN (chains A, D, G, J)
MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIK
FNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC
GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP
ALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

Sequence of entity 2 (B, E, H, K), FASTA

>1K5D_2 Ran-specific GTPase-activating protein (chains B, E, H, K)
MAAAKDTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIKTLEEDEEELFKMRAKLFRFAS
ENDLPEWKERGTGDVKLLKHKEKGAIRLLMRRDKTLKICANHYITPMMELKPNAGSDRAW
VWNTHADFADECPKPELLAIRFLNAENAQKFKTKFEECRKEIEEREKKAGSGKNDHAEKV
AEKLEALSVKEETKEDAEEKQ

Sequence of entity 3 (C, F, I, L), FASTA

>1K5D_3 Ran GTPase activating protein 1 (chains C, F, I, L)
MARFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKK
DLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSK
HTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWA
KTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIAL
KSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDE
KMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDMEELTDEEEEDEEEEAES
QSPEPETSEEEKEDKELADELSKAHI

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	4

Primary citation

RanGAP mediates GTP hydrolysis without an arginine finger. Seewald, M.J., Korner, C., Wittinghofer, A. et al. Nature (2002) 415:662-666. DOI 10.1038/415662a · PubMed

Other PDB entries of the same protein (UniProt P62826 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3GJ0 1.48 Å, Crystal structure of human RanGDP
7MO5 1.55 Å, Crystal Structure of the ZnF4 of Nucleoporin NUP153 in complex with Ran-GDP
7MO1 1.6 Å, Crystal Structure of the ZnF1 of Nucleoporin NUP153 in complex with Ran-GDP
5CIQ 1.65 Å, Ran GDP wild type tetragonal crystal form
7MO2 1.65 Å, Crystal Structure of the ZnF2 of Nucleoporin NUP153 in complex with Ran-GDP
5CIT 1.75 Å, Ran GDP wild type monoclinic crystal form
5CIW 1.75 Å, Ran GDP Y39A mutant monoclinic crystal form
5CJ2 1.75 Å, Ran GDP Y39A mutant triclinic crystal form
1I2M 1.76 Å, Ran-RCC1-SO4 complex
4HAT 1.78 Å, Crystal structure of CRM1 inhibitor Leptomycin B in complex with CRM1-Ran-RanBP1
3GJ3 1.79 Å, Crystal structure of human RanGDP-Nup153ZnF2 complex
3GJ5 1.79 Å, Crystal structure of human RanGDP-Nup153ZnF4 complex

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