6QIP: Serum albumin

Ternary complex of FcRn ectodomain, FcRn binding optimised human serum albumin and the albumin-biniding side chain of the human growth hormone derivative somapacitan. Determined by X-ray diffraction at 2.45 Å resolution. Released 5 Feb 2020.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,722
Mol. weight: 111.05 kDa
Ligands: JG5, CYS
Released: 5 Feb 2020

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

Secondary structure: helices and β-sheets

6QIP contains 53 α-helices and 29 β-strands across 3 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: 39 helices, 0 β-strands

Element	Residues	Length
α-helix	6-14	9
α-helix	16-30	15
α-helix	36-55	20
α-helix	66-77	12
α-helix	81-84	4
α-helix	85-92	8
α-helix	97-104	8
α-helix	116-119	4
α-helix	120-129	10
α-helix	131-145	15
α-helix	151-168	18
α-helix	174-201	28
α-helix	202-206	5
α-helix	208-222	15
α-helix	228-246	19
α-helix	250-265	16
α-helix	268-270	3
α-helix	278-280	3
α-helix	283-291	9
α-helix	293-299	7
α-helix	302-304	3
α-helix	306	1
α-helix	307-311	5
α-helix	315-321	7
α-helix	323-337	15
α-helix	343-360	18
α-helix	366-369	4
α-helix	373-376	4
α-helix	377-414	38
α-helix	420-437	18
α-helix	442-466	25
α-helix	471-479	9
α-helix	481-483	3
α-helix	484-490	7
α-helix	498-502	5
α-helix	511-515	5
α-helix	518-535	18
α-helix	541-560	20
α-helix	564-582	19

Chain B: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-14	9	1
α-helix	17-18	2
β-strand	24-30	7	1
β-strand	33-39	7	1
β-strand	46-47	2	1
α-helix	49-53	5
α-helix	56-57	2
α-helix	60-80	21
β-strand	89-99	11	1
β-strand	103-112	10	1
β-strand	115-121	7	1
β-strand	126-128	3	1
α-helix	132-142	11
α-helix	147-153	7
α-helix	154-158	5
α-helix	159-169	11
α-helix	171-174	4
β-strand	178	1	2
α-helix	179-180	2
β-strand	181-188	8	3
β-strand	193-203	11	3
β-strand	204	1	2
β-strand	209-214	6	4
β-strand	217-220	4	4
β-strand	223-228	6	3
β-strand	234-243	10	3
α-helix	247-249	3
β-strand	250-255	6	4
β-strand	263-265	3	4
α-helix	266-268	3

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-51	2	6
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serum albumin	A	protein	585	Homo sapiens	P02768 (AlphaFold model)
IgG receptor FcRn large subunit p51	B	protein	274	Homo sapiens	P55899 (AlphaFold model)
Beta-2-microglobulin	C	protein	105	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6QIP_1 Serum albumin (chains A)
DAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAE
NCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEV
DVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLP
KLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTK
VHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPA
DLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKC
CAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQMSA
PTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTES
LVNRRPCFSALEVDETYVPKEFNAGTFTFHADICTLSEKERQIKKQTALVELVKHKPKAT
KEQLKAAMDDFAAFVEKCCKADDKETCFAEEGKKLVAASQAALGL

Sequence of entity 2 (B), FASTA

>6QIP_2 IgG receptor FcRn large subunit p51 (chains B)
AESHLSLLYHLTAVSSPAPGTPAFWVSGWLGPQQYLSYNSLRGEAEPCGAWVWENQVSWY
WEKETTDLRIKEKLFLEAFKALGGKGPYTLQGLLGCELGPDNTSVPTAKFALNGEEFMNF
DLKQGTWGGDWPEALAISQRWQQQDKAANKELTFLLFSCPHRLREHLERGRGNLEWKEPP
SMRLKARPSSPGFSVLTCSAFSFYPPELQLRFLRNGLAAGTGQGDFGPNSDGSFHASSSL
TVKSGDEHHYCCIVQHAGLAQPLRVELESPAKSS

Sequence of entity 3 (C), FASTA

>6QIP_3 Beta-2-microglobulin (chains C)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
JG5	Somapacitan	C51 H89 N11 O19 S	1
CYS	Cysteine	C3 H7 N O2 S	1

Water and common crystallization additives (MES, BME) are not listed.

Primary citation

Identification of Binding Sites on Human Serum Albumin for Somapacitan, a Long-Acting Growth Hormone Derivative. Johansson, E., Nielsen, A.D., Demuth, H. et al. Biochemistry (2020) 59:1410-1419. DOI 10.1021/acs.biochem.0c00019 · PubMed

Other PDB entries of the same protein (UniProt P02768 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9IK6 1.69 Å, Human Serum Albumin crystallized with T4, pH 6.5
6YG9 1.89 Å, Crystal structure of human serum albumin (HSA) in complex with gn-07.
1N5U 1.9 Å, X-ray study of human serum albumin complexed with heme
8RCO 1.9 Å, Structure of Human Serum Albumin in complex with Aristolochic Acid II at 1.9 A resolution
8RCP 1.9 Å, Structure of Human Serum Albumin in complex with Myristic Acid
8RGK 1.9 Å, Structure of Human Serum Albumin in complex with Aristolochic Acid at 1.9 A resolution
8RGL 1.9 Å, Structure of Human Serum Albumin in complex with Aristolochic Acid I at 1.9 A resolution…
9EOD 1.9 Å, Human serum albumin with adamantene carboxylic acid
9CSG 1.91 Å, Human Serum Albumin Bound to Cerastecin Compound 5e
6QIO 1.95 Å, Ternary complex of FcRn ectodomain, FcRn binding optimised human serum albumin and the…
9IK7 1.97 Å, Human Serum Albumin crystallized with T4, pH 7.5
7VR0 1.98 Å, Human Serum Albumin

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