5K31: Collagen alpha-1 chain

Crystal structure of Human fibrillar procollagen type I C-propeptide Homo-trimer. Determined by X-ray diffraction at 2.2 Å resolution. Released 22 Mar 2017.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 6
Atoms: 11,547
Mol. weight: 172.93 kDa
Ligands: CA
Released: 22 Mar 2017

Explore 5K31 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5K31 contains 46 α-helices and 118 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: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	9-28	20
β-strand	38	1	1
α-helix	41-47	7
α-helix	51-52	2
β-strand	54-58	5	1
α-helix	65-67	3
β-strand	69-74	6	1
β-strand	79-82	4	1
β-strand	84	1	2
β-strand	88-92	5	1
β-strand	96	1	3
α-helix	108-111	4
β-strand	120	1	2
α-helix	127-139	13
β-strand	144-153	10	1
β-strand	171-173	3	4
β-strand	179-180	2	4
β-strand	181	1	5
β-strand	189	1	5
β-strand	191-195	5	1
β-strand	204-213	10	1
α-helix	216-218	3
β-strand	223-225	3	4
β-strand	230	1	3
β-strand	235-245	11	1

Chain B: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	13-28	16
β-strand	38	1	6
α-helix	41-47	7
β-strand	54-58	5	6
α-helix	65-67	3
β-strand	69-74	6	6
β-strand	79-82	4	6
α-helix	83	1
β-strand	84	1	7
β-strand	88-92	5	6
β-strand	96	1	8
α-helix	108-111	4
α-helix	117-119	3
β-strand	120	1	7
α-helix	127-139	13
β-strand	144-153	10	6
β-strand	160	1	9
β-strand	165	1	9
β-strand	171-174	4	10
β-strand	179-180	2	10
β-strand	181	1	11
β-strand	189	1	11
β-strand	191-195	5	6
β-strand	204-213	10	6
α-helix	216-218	3
β-strand	221-225	5	10
β-strand	230	1	8
β-strand	235-245	11	6

Chain C: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	11-28	18
β-strand	38	1	12
α-helix	41-47	7
β-strand	54-58	5	12
α-helix	65-67	3
β-strand	69-74	6	12
β-strand	79-82	4	12
α-helix	83	1
β-strand	84	1	13
β-strand	88-92	5	12
β-strand	96	1	14
α-helix	108-111	4
β-strand	120	1	13
α-helix	127-139	13
β-strand	144-153	10	12
β-strand	160	1	15
β-strand	165	1	15
β-strand	171-174	4	16
β-strand	179-180	2	16
β-strand	181	1	17
α-helix	186-188	3
β-strand	189	1	17
β-strand	191-195	5	12
β-strand	204-213	10	12
α-helix	216-218	3
β-strand	221-225	5	16
β-strand	230	1	14
β-strand	235-245	11	12

Chain D: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	12-28	17
β-strand	38	1	18
α-helix	41-47	7
β-strand	54-58	5	18
α-helix	65-67	3
β-strand	69-74	6	18
β-strand	79-82	4	18
α-helix	83	1
β-strand	84	1	19
β-strand	88-92	5	18
β-strand	96	1	20
α-helix	108-111	4
β-strand	120	1	19
α-helix	127-139	13
β-strand	144-153	10	18
β-strand	160	1	21
β-strand	165	1	21
β-strand	171-173	3	22
β-strand	179-180	2	22
β-strand	181	1	23
α-helix	186-188	3
β-strand	189	1	23
β-strand	191-195	5	18
β-strand	204-213	10	18
α-helix	216-218	3
β-strand	223-225	3	22
β-strand	230	1	20
β-strand	235-245	11	18

Chain E: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	10-28	19
β-strand	38	1	24
α-helix	41-47	7
α-helix	51-52	2
β-strand	54-58	5	24
β-strand	69-74	6	24
β-strand	79-82	4	24
β-strand	84	1	25
β-strand	88-92	5	24
β-strand	96	1	26
α-helix	108-111	4
α-helix	117-119	3
β-strand	120	1	25
α-helix	127-139	13
β-strand	144-153	10	24
β-strand	160	1	27
β-strand	165	1	27
β-strand	171-173	3	28
β-strand	175	1	29
β-strand	177	1	29
β-strand	179-180	2	28
β-strand	181	1	30
α-helix	186-188	3
β-strand	189	1	30
β-strand	191-195	5	24
β-strand	204-213	10	24
α-helix	216-218	3
β-strand	223-225	3	28
β-strand	230	1	26
β-strand	235-245	11	24

Chain F: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	10-28	19
β-strand	38	1	31
α-helix	41-47	7
α-helix	51-52	2
β-strand	54-58	5	31
α-helix	65-67	3
β-strand	69-74	6	31
β-strand	79-82	4	31
β-strand	84	1	32
β-strand	88-92	5	31
β-strand	96	1	33
α-helix	108-111	4
β-strand	120	1	32
α-helix	127-139	13
β-strand	144-153	10	31
β-strand	171-173	3	34
β-strand	179-180	2	34
β-strand	181	1	35
β-strand	189	1	35
β-strand	191-195	5	31
β-strand	205-213	9	31
α-helix	216-218	3
β-strand	223-225	3	34
β-strand	230	1	33
β-strand	235-245	11	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Collagen alpha-1(I) chain	A, B, C, D, E, F	protein	255	Homo sapiens	P02452 (AlphaFold model)

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

>5K31_1 Collagen alpha-1(I) chain (chains A, B, C, D, E, F)
ETGHHHHHHDDANVVRDRDLEVDTTLKSLSQQIENIRSPEGSRKNPARTCRDLKMCHSDW
KSGEYWIDPNQGCNLDAIKVFCNMETGETCVYPTQPSVAQKNWYISKNPKDKRHVWFGES
MTDGFQFEYGGQGSDPADVAIQLTFLRLMSTEASQQITYHCKNSVAYMDQQTGNLKKALL
LQGSNEIEIRAEGNSRFTYSVTVDGCTSHTGAWGKTVIEYKTTKSSRLPIIDVAPLDVGA
PDQEFGFDVGPVCFL

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	6

Water and common crystallization additives (CL, GOL) are not listed.

Primary citation

Structural basis of homo- and heterotrimerization of collagen I. Sharma, U., Carrique, L., Vadon-Le Goff, S. et al. Nat Commun (2017) 8:14671-14671. DOI 10.1038/ncomms14671 · PubMed

Other PDB entries of the same protein (UniProt P02452 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5CTD 1.6 Å, Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest…
8YV3 1.68 Å, The heterotrimer structure of peptides derived from human collagen type I
1Q7D 1.8 Å, Structure of the integrin alpha2beta1 binding collagen peptide
5CTI 1.9 Å, Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest…
5CVA 2.1 Å, Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest…
3EJH 2.1 Å, Crystal Structure of the Fibronectin 8-9FnI Domain Pair in Complex with a Type-I…
5CVB 2.25 Å, Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest…
5OU8 2.5 Å, Crystal structure of Glycoprotein VI in complex with collagen-peptide (GPO)5
5OU9 2.5 Å, Crystal structure of Glycoprotein VI in complex with collagen-peptide (GPO)3
3GXE 2.6 Å, Complex of a Low Affinity Collagen Site with the Fibronectin 8-9FnI Domain Pair
7E7B 2.6 Å, Cryo-EM structure of the SARS-CoV-2 furin site mutant S-Trimer from a subunit vaccine…
7E7D 3.2 Å, Cryo-EM structure of the SARS-CoV-2 wild-type S-Trimer from a subunit vaccine candidate

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