4KFZ: LMO2 and anti-LMO2 VH complex

Name: PDB 4KFZ: Crystal structure of LMO2 and anti-LMO2 VH complex
Published: 2014-01-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of LMO2 and anti-LMO2 VH complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 22 Jan 2014.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,350
Mol. weight: 63.62 kDa
Ligands: ZN
Released: 22 Jan 2014

Explore 4KFZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KFZ contains 25 α-helices and 58 β-strands across 4 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: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	22-24	3
β-strand	29	1	1
β-strand	30	1	2
β-strand	36	1	1
β-strand	43-45	3	2
β-strand	48-50	3	2
β-strand	56	1	3
β-strand	63	1	3
β-strand	72-74	3	4
β-strand	77-79	3	4
α-helix	81-87	7
β-strand	93	1	5
β-strand	100	1	5
α-helix	101-102	2
β-strand	107-110	4	6
β-strand	113-116	4	6
β-strand	121	1	7
α-helix	127	1
β-strand	128	1	7
α-helix	129-130	2
β-strand	135-138	4	8
β-strand	141-144	4	8
α-helix	145-155	11

Chain B: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	22-24	3
β-strand	29	1	9
β-strand	30	1	10
β-strand	36	1	9
β-strand	43-45	3	10
β-strand	48-50	3	10
β-strand	56	1	11
α-helix	62	1
β-strand	63	1	11
β-strand	72-74	3	12
β-strand	77-79	3	12
α-helix	81-87	7
β-strand	93	1	13
β-strand	100	1	13
α-helix	101-102	2
β-strand	107-110	4	14
β-strand	113-116	4	14
β-strand	121	1	15
α-helix	127	1
β-strand	128	1	15
α-helix	129-130	2
β-strand	135-138	4	16
β-strand	141-144	4	16
α-helix	145-155	11

Chain C: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	-1-2	4
β-strand	3-7	5	17
β-strand	10-12	3	18
β-strand	18-25	8	17
α-helix	29-31	3
β-strand	34-39	6	18
β-strand	46-51	6	18
β-strand	58-60	3	18
α-helix	62-64	3
β-strand	68-73	6	17
β-strand	78-83	6	17
α-helix	88-90	3
β-strand	92-98	7	18
α-helix	99-100	2
β-strand	105-107	3	6
α-helix	110-113	4
β-strand	114	1	18
β-strand	118-122	5	18

Chain D: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	0-2	3
β-strand	3-7	5	19
β-strand	10-12	3	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	34-39	6	20
β-strand	45-51	7	20
β-strand	58-60	3	20
α-helix	62-64	3
β-strand	68-73	6	19
β-strand	78-83	6	19
α-helix	88-90	3
β-strand	92-98	7	20
α-helix	99-100	2
β-strand	105-107	3	14
α-helix	110-113	4
β-strand	114	1	20
β-strand	118-122	5	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
LMO-2	A, B	protein	150	Homo sapiens	P25791 (AlphaFold model)
Anti-LMO2 VH	C, D	protein	129	Homo sapiens	P01764 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4KFZ_1 LMO-2 (chains A, B)
SLDPSEEPVDEVLQIPPSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVG
RRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKH
FCVGDRYLLINSDIVCEQDIYEWTKINGMI

Sequence of entity 2 (C, D), FASTA

>4KFZ_2 Anti-LMO2 VH (chains C, D)
GGSMAEVQLLESGGGLVQPGGSLRLSCAASGFSFSHSPMNWVRQAPGKGLEWVSYISYNS
SSIYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGLTESLELTADWFDYWG
QGTLVTVSS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

Conformational flexibility of the oncogenic protein LMO2 primes the formation of the multi-protein transcription complex. Sewell, H., Tanaka, T., Omari, K.E. et al. Sci Rep (2014) 4:3643-3643. DOI 10.1038/srep03643 · PubMed

Other PDB entries of the same protein (UniProt P25791 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2XJY 2.4 Å, Crystal structure of the LMO2:LDB1-LID complex, P21 crystal form
2XJZ 2.8 Å, Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form
2YPA 2.8 Å, Structure of the SCL:E47:LMO2:LDB1 complex bound to DNA

Browse structure collections

About this viewer

MolViewer shows 4KFZ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.