3V83: Serotransferrin

The 2.1 angstrom crystal structure of diferric human transferrin. Determined by X-ray diffraction at 2.1 Å resolution. Released 15 Feb 2012.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 6
Atoms: 33,928
Mol. weight: 472.51 kDa
Ligands: BCT, FE
Released: 15 Feb 2012

Explore 3V83 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V83 contains 246 α-helices and 173 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: 41 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	1
α-helix	12-27	16
β-strand	36-42	7	1
α-helix	45-53	9
β-strand	59	1	1
β-strand	60-62	3	2
α-helix	64-71	8
β-strand	77-84	8	2
β-strand	85-86	2	3
β-strand	91-92	2	3
β-strand	94-102	9	4
α-helix	109-111	3
β-strand	117-119	3	4
α-helix	125-129	5
α-helix	130-135	6
α-helix	136-138	3
α-helix	140	1
α-helix	142	1
α-helix	146-153	8
β-strand	157-158	2	4
α-helix	168-171	4
α-helix	187-196	10
β-strand	202-206	5	4
α-helix	209-213	5
α-helix	217-220	4
β-strand	223-226	4	4
β-strand	232-233	2	4
α-helix	235-240	6
β-strand	244-247	4	4
α-helix	248-249	2
β-strand	250-254	5	2
α-helix	260-274	15
β-strand	301-304	4	2
α-helix	305-306	2
α-helix	311-315	5
α-helix	317-327	11
α-helix	335-338	4
α-helix	340-341	2
β-strand	342-347	6	5
α-helix	348-361	14
β-strand	366-371	6	5
α-helix	374-383	10
β-strand	388-391	4	5
α-helix	393-401	9
β-strand	405-411	7	5
α-helix	418-420	3
β-strand	426-433	8	6
β-strand	448-451	4	6
α-helix	457-461	5
α-helix	462-471	10
α-helix	476-479	4
β-strand	482-484	3	6
α-helix	493-495	3
α-helix	502-504	3
α-helix	516-526	11
β-strand	530-534	5	6
α-helix	537-540	4
α-helix	556-558	3
β-strand	559-561	3	6
β-strand	570	1	6
α-helix	571-576	6
β-strand	580-582	3	6
α-helix	583-585	3
β-strand	586-589	4	5
α-helix	591-593	3
α-helix	594-608	15
β-strand	637-640	4	5
α-helix	647-651	5
α-helix	653-660	8
α-helix	669-674	6

Chain B: 41 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	7
α-helix	12-29	18
β-strand	36-42	7	7
α-helix	45-53	9
β-strand	59	1	7
β-strand	60-62	3	8
α-helix	64-71	8
β-strand	77-85	9	8
β-strand	92	1	8
β-strand	94-102	9	9
α-helix	109-111	3
β-strand	117-119	3	9
α-helix	125-129	5
α-helix	130-135	6
α-helix	136-138	3
α-helix	140	1
α-helix	142	1
α-helix	146-153	8
β-strand	157-158	2	9
α-helix	168-171	4
α-helix	187-196	10
β-strand	202-206	5	9
α-helix	209-213	5
α-helix	217-220	4
β-strand	223-226	4	9
β-strand	232-233	2	9
α-helix	235-240	6
β-strand	244-247	4	9
α-helix	248-249	2
β-strand	250-254	5	8
α-helix	260-274	15
β-strand	299-304	6	8
α-helix	305-306	2
α-helix	311-315	5
α-helix	317-328	12
α-helix	340-341	2
β-strand	342-347	6	10
α-helix	348-362	15
β-strand	366-371	6	10
α-helix	374-383	10
β-strand	388-391	4	10
α-helix	393-401	9
β-strand	405-411	7	10
α-helix	418-420	3
β-strand	426-433	8	11
β-strand	448-451	4	11
α-helix	457-461	5
α-helix	462-471	10
α-helix	476-479	4
β-strand	482-484	3	11
α-helix	493-495	3
α-helix	502-504	3
α-helix	516-526	11
β-strand	530-534	5	11
α-helix	537-541	5
α-helix	556-558	3
β-strand	559-562	4	11
β-strand	568-570	3	11
α-helix	571-576	6
β-strand	580-582	3	11
α-helix	583-585	3
β-strand	586-589	4	10
α-helix	591-593	3
α-helix	594-608	15
β-strand	637-639	3	10
α-helix	647-651	5
α-helix	653-661	9
α-helix	663-665	3
α-helix	669-674	6

Chain C: 38 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	12
α-helix	12-29	18
β-strand	36-42	7	12
α-helix	45-53	9
β-strand	59	1	12
β-strand	60-62	3	13
α-helix	64-71	8
β-strand	77-85	9	13
β-strand	92	1	13
β-strand	94-102	9	14
α-helix	109-111	3
β-strand	117-119	3	14
α-helix	125-129	5
α-helix	130-135	6
α-helix	136-138	3
α-helix	140	1
α-helix	146-153	8
β-strand	157-158	2	14
α-helix	168-171	4
α-helix	187-197	11
β-strand	202-206	5	14
α-helix	209-213	5
α-helix	217-220	4
β-strand	223-226	4	14
β-strand	232-234	3	14
α-helix	235-240	6
β-strand	244-247	4	14
α-helix	248-249	2
β-strand	250-254	5	13
α-helix	260-274	15
β-strand	299-304	6	13
α-helix	305-306	2
α-helix	311-315	5
α-helix	317-327	11
α-helix	332-334	3
α-helix	339-341	3
β-strand	342-347	6	15
α-helix	348-361	14
β-strand	366-371	6	15
α-helix	374-382	9
β-strand	388-391	4	15
α-helix	393-401	9
β-strand	405-411	7	15
β-strand	426-433	8	16
α-helix	442-444	3
β-strand	450	1	16
α-helix	457-461	5
α-helix	462-471	10
α-helix	476-479	4
β-strand	484	1	16
β-strand	495	1	16
α-helix	502-504	3
α-helix	516-526	11
β-strand	531-534	4	16
α-helix	537-540	4
α-helix	556-558	3
β-strand	559-561	3	16
β-strand	570	1	16
α-helix	574-576	3
β-strand	580-582	3	16
α-helix	583-585	3
β-strand	586-589	4	15
α-helix	594-607	14
β-strand	637-640	4	15
α-helix	647-651	5
α-helix	653-660	8
α-helix	669-674	6

Chain D: 41 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	17
α-helix	12-29	18
β-strand	36-42	7	17
α-helix	45-53	9
β-strand	59	1	17
β-strand	60-62	3	18
α-helix	64-71	8
β-strand	77-84	8	18
β-strand	85-86	2	19
β-strand	91-92	2	19
β-strand	94-102	9	20
α-helix	109-111	3
β-strand	117-119	3	20
α-helix	125-129	5
α-helix	130-135	6
α-helix	136-138	3
α-helix	146-153	8
β-strand	157-158	2	20
α-helix	168-171	4
α-helix	187-196	10
β-strand	202-206	5	20
α-helix	209-213	5
α-helix	217-220	4
β-strand	223-226	4	20
β-strand	232-233	2	20
α-helix	238-240	3
β-strand	244-247	4	20
α-helix	248-249	2
β-strand	250-254	5	18
α-helix	260-274	15
β-strand	301-304	4	18
α-helix	305-306	2
α-helix	311-315	5
α-helix	317-328	12
α-helix	340-341	2
β-strand	342-347	6	21
α-helix	348-361	14
β-strand	366-371	6	21
α-helix	374-383	10
β-strand	388-391	4	21
α-helix	393-401	9
β-strand	405-411	7	21
α-helix	418-420	3
β-strand	426-433	8	22
α-helix	441-443	3
β-strand	448-451	4	22
α-helix	457-461	5
α-helix	462-471	10
α-helix	476-479	4
β-strand	482-484	3	22
α-helix	493-495	3
α-helix	502-504	3
α-helix	516-526	11
β-strand	530-534	5	22
α-helix	537-540	4
α-helix	549-552	4
α-helix	556-558	3
β-strand	559-561	3	22
α-helix	562-563	2
β-strand	570	1	22
α-helix	571-573	3
β-strand	580-582	3	22
α-helix	583-585	3
β-strand	586-589	4	21
α-helix	594-608	15
β-strand	637-639	3	21
α-helix	647-651	5
α-helix	653-661	9
α-helix	663-665	3
α-helix	669-674	6

Chain E: 43 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	23
α-helix	12-29	18
β-strand	36-42	7	23
α-helix	45-53	9
β-strand	59	1	23
β-strand	60-62	3	24
α-helix	64-71	8
β-strand	77-84	8	24
β-strand	85-86	2	25
β-strand	91-92	2	25
β-strand	94-102	9	26
α-helix	109-111	3
β-strand	117-119	3	26
α-helix	125-129	5
α-helix	130-135	6
α-helix	136-138	3
α-helix	140	1
α-helix	142	1
α-helix	146-153	8
β-strand	157-158	2	26
α-helix	168-171	4
α-helix	187-196	10
β-strand	202-206	5	26
α-helix	209-213	5
α-helix	217-220	4
β-strand	223-226	4	26
β-strand	232-234	3	26
α-helix	238-240	3
β-strand	244-247	4	26
α-helix	248-249	2
β-strand	250-254	5	24
α-helix	260-274	15
β-strand	301-304	4	24
α-helix	305-306	2
α-helix	311-315	5
α-helix	317-327	11
α-helix	332-334	3
α-helix	340-341	2
β-strand	342-347	6	27
α-helix	348-361	14
β-strand	366-371	6	27
α-helix	374-383	10
β-strand	388-391	4	27
α-helix	393-401	9
β-strand	405-411	7	27
α-helix	418-420	3
β-strand	426-433	8	28
α-helix	441-443	3
β-strand	449-451	3	28
α-helix	457-461	5
α-helix	462-471	10
α-helix	476-479	4
β-strand	483-484	2	28
α-helix	493-495	3
α-helix	502-504	3
α-helix	516-526	11
β-strand	530-534	5	28
α-helix	537-540	4
α-helix	556-558	3
β-strand	559-562	4	28
β-strand	568-570	3	28
α-helix	571-576	6
β-strand	580-582	3	28
α-helix	583-585	3
β-strand	586-589	4	27
α-helix	591-593	3
α-helix	594-608	15
β-strand	637-639	3	27
α-helix	647-651	5
α-helix	653-660	8
α-helix	663-665	3
α-helix	669-674	6

Chain F: 42 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	29
α-helix	12-29	18
β-strand	36-42	7	29
α-helix	45-53	9
β-strand	59	1	29
β-strand	60-62	3	30
α-helix	64-71	8
β-strand	77-84	8	30
β-strand	85	1	31
β-strand	92	1	31
β-strand	94-102	9	32
α-helix	109-111	3
β-strand	117-119	3	32
α-helix	125-129	5
α-helix	130-135	6
α-helix	136-138	3
α-helix	140	1
α-helix	142	1
α-helix	146-153	8
β-strand	157-158	2	32
α-helix	168-171	4
α-helix	187-196	10
β-strand	202-206	5	32
α-helix	209-213	5
α-helix	217-220	4
β-strand	223-226	4	32
β-strand	232-233	2	32
α-helix	235-240	6
β-strand	244-247	4	32
α-helix	248-249	2
β-strand	250-254	5	30
α-helix	260-274	15
β-strand	301-304	4	30
α-helix	305-306	2
α-helix	311-315	5
α-helix	317-327	11
α-helix	339-341	3
β-strand	342-347	6	33
α-helix	348-361	14
β-strand	366-371	6	33
α-helix	374-383	10
β-strand	388-391	4	33
α-helix	393-401	9
β-strand	405-411	7	33
β-strand	426-433	8	34
α-helix	441-443	3
β-strand	448-451	4	34
α-helix	457-461	5
α-helix	462-471	10
α-helix	476-479	4
β-strand	482-484	3	34
α-helix	493-495	3
α-helix	502-504	3
α-helix	516-526	11
β-strand	530-534	5	34
α-helix	537-540	4
α-helix	549-552	4
α-helix	556-558	3
β-strand	559-562	4	34
α-helix	563	1
β-strand	568-570	3	34
α-helix	571-576	6
β-strand	580-582	3	34
α-helix	583-585	3
β-strand	586-589	4	33
α-helix	591-593	3
α-helix	594-608	15
β-strand	637-639	3	33
α-helix	647-661	15
α-helix	663-665	3
α-helix	669-673	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serotransferrin	A, B, C, D, E, F	protein	698	Homo sapiens	P02787 (AlphaFold model)

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

>3V83_1 Serotransferrin (chains A, B, C, D, E, F)
MRLAVGALLVCAVLGLCLAVPDKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVK
KASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFYYAVAVV
KKDSGFQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVANFFSGSCAPC
ADGTDFPQLCQLCPGCGCSTLNQYFGYSGAFKCLKDGAGDVAFVKHSTIFENLANKADRD
QYELLCLDNTRKPVDEYKDCHLAQVPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKE
FQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLGYEYVTAIRNLREGTCPEAPTDECKP
VKWCALSHHERLKCDEWSVNSVGKIECVSAETTEDCIAKIMNGEADAMSLDGGFVYIAGK
CGLVPVLAENYNKSDNCEDTPEAGYFAVAVVKKSASDLTWDNLKGKKSCHTAVGRTAGWN
IPMGLLYNKINHCRFDEFFSEGCAPGSKKDSSLCKLCMGSGLNLCEPNNKEGYYGYTGAF
RCLVEKGDVAFVKHQTVPQNTGGKNPDPWAKNLNEKDYELLCLDGTRKPVEEYANCHLAR
APNHAVVTRKDKEACVHKILRQQQHLFGSNVTDCSGNFCLFRSETKDLLFRDDTVCLAKL
HDRNTYEKYLGEEYVKAVGNLRKCSTSSLLEACTFRRP

Ligands and cofactors

ID	Name	Formula	Copies
BCT	Bicarbonate ion	C H O3	12
FE	FE (III) ion	Fe	12

Water and common crystallization additives (P6G, SO4) are not listed.

Primary citation

Structural basis for iron piracy by pathogenic Neisseria. Noinaj, N., Easley, N.C., Oke, M. et al. Nature (2012) 483:53-58. DOI 10.1038/nature10823 · PubMed

Other PDB entries of the same protein (UniProt P02787 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1RYO 1.2 Å, Human serum transferrin, N-lobe bound with oxalate
1A8E 1.6 Å, Human serum transferrin, recombinant N-terminal lobe
3SKP 1.7 Å, The structure of apo-human transferrin C-lobe with bound sulfate ions
1A8F 1.8 Å, Human serum transferrin, recombinant N-terminal lobe
1D3K 1.8 Å, Human serum transferrin
1FQE 1.8 Å, Crystal structures of mutant (K206A) that abolish the dilysine interaction in the N-lobe…
3FGS 1.8 Å, Crystal structure of G65R/K206E double mutant of the N-lobe human transferrin
1JQF 1.85 Å, Human Transferrin N-Lobe Mutant H249Q
1OQG 1.9 Å, Crystal structure of the D63E mutant of the N-lobe human transferrin
9RTB 1.93 Å, Crystal structure of the adduct formed upon reaction of [V(IV)O(acetylacetonate)2] with…
1D4N 2.0 Å, Human serum transferrin
1N84 2.05 Å, Human serum transferrin, N-lobe

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