2BDI: Kallikrein-4

Human Kallikrein 4 complex with cobalt and p-aminobenzamidine. Determined by X-ray diffraction at 3.0 Å resolution. Released 3 Oct 2006.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 16
Atoms: 27,340
Mol. weight: 385.23 kDa
Ligands: PBZ, CO
Released: 3 Oct 2006

Explore 2BDI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2BDI contains 157 α-helices and 303 β-strands across 16 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-34	5	3
β-strand	40-48	9	3
β-strand	51-54	4	3
α-helix	56-58	3
β-strand	63-67	5	3
β-strand	72	1	4
α-helix	74A-76	3
β-strand	81-82	2	3
β-strand	85-90	6	3
β-strand	104-108	5	3
α-helix	122	1
β-strand	123	1	2
α-helix	124	1
β-strand	135-140	6	2
α-helix	142-144	3
β-strand	154	1	4
β-strand	156-162	7	2
α-helix	163-164	2
α-helix	165-172	8
β-strand	180-183	4	2
β-strand	189	1	1
β-strand	198-201	4	2
β-strand	208-215	8	2
β-strand	226-230	5	2
α-helix	231-233	3
α-helix	235-242	8

Chain B: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	5
β-strand	20-21	2	6
α-helix	22-23	2
β-strand	30-34	5	7
β-strand	40-48	9	7
β-strand	51-54	4	7
α-helix	56-58	3
β-strand	63-67	5	7
β-strand	72	1	8
α-helix	74A-76	3
β-strand	81-82	2	7
β-strand	85-90	6	7
β-strand	104-108	5	7
α-helix	122	1
β-strand	123	1	6
α-helix	124	1
α-helix	128-129	2
β-strand	135-140	6	6
β-strand	154	1	8
β-strand	156-162	7	6
α-helix	163-164	2
α-helix	165-172	8
β-strand	180-183	4	6
β-strand	189	1	5
β-strand	198-201	4	6
β-strand	208-215	8	6
α-helix	225	1
β-strand	226-230	5	6
α-helix	231-234	4
α-helix	235-242	8

Chains C and J: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	9
β-strand	20-21	2	10
α-helix	22-23	2
β-strand	30-34	5	11
β-strand	40-48	9	11
β-strand	51-54	4	11
α-helix	56-58	3
β-strand	63-67	5	11
β-strand	72	1	12
α-helix	74A-76	3
β-strand	81-82	2	11
β-strand	85-90	6	11
β-strand	104-108	5	11
α-helix	122	1
β-strand	123	1	10
α-helix	124	1
α-helix	128-129	2
β-strand	135-140	6	10
β-strand	154	1	12
β-strand	156-162	7	10
α-helix	163-164	2
α-helix	165-172	8
β-strand	180-183	4	10
β-strand	189	1	9
β-strand	198-201	4	10
β-strand	208-215	8	10
α-helix	225	1
β-strand	226-230	5	10
α-helix	231-233	3
α-helix	235-242	8

Chains D, H, N and P: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	13
β-strand	20-21	2	14
α-helix	22-23	2
β-strand	30-34	5	15
β-strand	40-48	9	15
β-strand	51-54	4	15
α-helix	56-58	3
β-strand	63-67	5	15
β-strand	72	1	16
α-helix	74A-76	3
β-strand	81-82	2	15
β-strand	85-90	6	15
β-strand	104-108	5	15
α-helix	122	1
β-strand	123	1	14
α-helix	124	1
β-strand	135-140	6	14
β-strand	154	1	16
β-strand	156-162	7	14
α-helix	163-164	2
α-helix	165-172	8
β-strand	180-183	4	14
β-strand	189	1	13
β-strand	198-201	4	14
β-strand	208-215	8	14
α-helix	225	1
β-strand	226-230	5	14
α-helix	231-233	3
α-helix	235-242	8

Chain E: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	17
β-strand	20-21	2	18
α-helix	22-23	2
β-strand	30-34	5	19
β-strand	40-48	9	19
β-strand	51-54	4	19
α-helix	56-58	3
β-strand	63-67	5	19
β-strand	72	1	20
α-helix	74A-76	3
β-strand	81-82	2	19
β-strand	85-90	6	19
β-strand	104-108	5	19
α-helix	122	1
β-strand	123	1	18
α-helix	124	1
β-strand	135-140	6	18
β-strand	154	1	20
β-strand	156-162	7	18
α-helix	163-164	2
α-helix	165-172	8
β-strand	180-183	4	18
β-strand	189	1	17
β-strand	198-201	4	18
β-strand	208-215	8	18
β-strand	226-230	5	18
α-helix	231-234	4
α-helix	235-242	8

Chain F: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	21
β-strand	20-21	2	22
β-strand	30-34	5	23
β-strand	40-48	9	23
β-strand	51-54	4	23
α-helix	56-58	3
β-strand	63-67	5	23
β-strand	72	1	24
α-helix	74A-76	3
β-strand	81-82	2	23
β-strand	85-90	6	23
β-strand	104-108	5	23
α-helix	122	1
β-strand	123	1	22
α-helix	124	1
β-strand	135-140	6	22
β-strand	154	1	24
β-strand	156-162	7	22
α-helix	163-164	2
α-helix	165-171	7
β-strand	180-183	4	22
β-strand	189	1	21
β-strand	198-201	4	22
β-strand	208-215	8	22
α-helix	225	1
β-strand	226-230	5	22
α-helix	231-234	4
α-helix	235-242	8

Chain G: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	25
β-strand	20-21	2	26
α-helix	22-23	2
β-strand	30-34	5	27
β-strand	40-48	9	27
β-strand	51-54	4	27
α-helix	56-58	3
β-strand	63-67	5	27
β-strand	72	1	28
α-helix	74A-76	3
β-strand	81-82	2	27
β-strand	85-90	6	27
β-strand	104-108	5	27
α-helix	122	1
β-strand	123	1	26
α-helix	124	1
β-strand	135-140	6	26
β-strand	154	1	28
β-strand	156-162	7	26
α-helix	163-164	2
α-helix	165-172	8
β-strand	180-183	4	26
β-strand	189	1	25
β-strand	198-200	3	26
β-strand	209-215	7	26
α-helix	225	1
β-strand	226-230	5	26
α-helix	231-233	3
α-helix	235-242	8

Chain I: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	33
β-strand	20-21	2	34
α-helix	22-23	2
β-strand	30-34	5	35
β-strand	40-48	9	35
β-strand	51-54	4	35
α-helix	56-58	3
β-strand	63-67	5	35
β-strand	72	1	36
α-helix	74A-76	3
β-strand	81-82	2	35
β-strand	85-90	6	35
β-strand	104-108	5	35
α-helix	122	1
β-strand	123	1	34
α-helix	124	1
β-strand	135-140	6	34
β-strand	154	1	36
β-strand	156-162	7	34
α-helix	163-164	2
α-helix	165-172	8
β-strand	180-183	4	34
β-strand	189	1	33
β-strand	198-201	4	34
β-strand	208-215	8	34
β-strand	226-230	5	34
α-helix	231-233	3
α-helix	235-242	8

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kallikrein-4	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	protein	223	Homo sapiens	Q9Y5K2 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P), FASTA

>2BDI_1 Kallikrein-4 (chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P)
IINGEDCSPHSQPWQAALVMENELFCSGVLVHPQWVLSAAHCFQNSYTIGLGLHSLEADQ
EPGSQMVEASLSVRHPEYNRPLLANDLMLIKLDESVSESDTIRSISIASQCPTAGNSCLV
SGWGLLANGRMPTVLQCVNVSVVSEEVCSKLYDPLYHPSMFCAGGGQDQKDSCNGDSGGP
LICNGYLQGLVSFGKAPCGQVGVPGVYTNLCKFTEWIEKTVQA

Ligands and cofactors

ID	Name	Formula	Copies
PBZ	P-amino benzamidine	C7 H10 N3	16
CO	Cobalt (II) ion	Co	4

Primary citation

Crystal structures of human tissue kallikrein 4: activity modulation by a specific zinc binding site. Debela, M., Magdolen, V., Grimminger, V. et al. J Mol Biol (2006) 362:1094-1107. DOI 10.1016/j.jmb.2006.08.003 · PubMed

Other PDB entries of the same protein (UniProt Q9Y5K2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4K8Y 1.0 Å, Atomic resolution crystal structures of Kallikrein-Related Peptidase 4 complexed with…
4KEL 1.15 Å, Atomic resolution crystal structure of Kallikrein-Related Peptidase 4 complexed with a…
6O21 1.15 Å, Crystal Structure of Human KLK4 in Complex With Cleaved SFTI-FCQR(Asn14)[1,14] Inhibitor
4K1E 1.3 Å, Atomic resolution crystal structures of Kallikrein-Related Peptidase 4 complexed with a…
7JOD 1.33 Å, Crystal structure of BbKI complexed with Human Kallikrein 4
7JQK 1.33 Å, Crystal structure of the R64A mutant of Bauhinia Bauhinioides Kallikrein Inhibitor…
7JQN 1.5 Å, Crystal structure of the R64M mutant of Bauhinia Bauhinioides Kallikrein Inhibitor…
7JQO 1.6 Å, Crystal structure of the R64D mutant of Bauhinia Bauhinioides Kallikrein Inhibitor…
6NVB 1.64 Å, Crystal structure of the inhibitor-free form of the serine protease kallikrein-4
7JOW 1.91 Å, Crystal structure of BbKI complexed with Human Kallikrein 4
2BDG 1.95 Å, Human Kallikrein 4 complex with nickel and p-aminobenzamidine
6KBR 2.0 Å, Crystal structure of Human KLK4 and SPINK2 derived KLK4 inhibitor complex

Browse structure collections

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