4LMQ: Stromal cell-derived factor 1

Development and Preclinical Characterization of a Humanized Antibody Targeting CXCL12. Determined by X-ray diffraction at 2.77 Å resolution. Released 14 Aug 2013.

Method: X-ray diffraction
Resolution: 2.77 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,398
Mol. weight: 108.21 kDa
Released: 14 Aug 2013

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

Secondary structure: helices and β-sheets

4LMQ contains 34 α-helices and 95 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 D: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
β-strand	23-29	7	1
β-strand	38-42	5	1
β-strand	48-50	3	1
α-helix	51-52	2
α-helix	56-65	10

Chain E: 3 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	2
β-strand	11-12	2	3
β-strand	18-25	8	2
β-strand	34-40	7	4
β-strand	44-51	8	4
β-strand	57-59	3	4
β-strand	67-68	2	2
β-strand	71-72	2	2
β-strand	77-82	6	2
α-helix	84-86	3
β-strand	88-95	8	4
β-strand	100D-103	4	4
β-strand	107-109	3	4
β-strand	110-111	2	3
β-strand	120-123	4	5
β-strand	139-145	7	5
β-strand	151-154	4	6
β-strand	159	1	6
β-strand	164-165	2	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-181	6	5
β-strand	195-200	6	6
α-helix	201-203	3
β-strand	205-210	6	6

Chain F: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	14-15	2	1
α-helix	17-19	3
α-helix	20-22	3
β-strand	23-28	6	1
β-strand	38-42	5	1
β-strand	48-51	4	1
α-helix	56-63	8

Chain H: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
β-strand	34-39	6	8
β-strand	45-51	7	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-95	8	8
β-strand	100D-103	4	8
β-strand	104	1	7
β-strand	107-111	5	8
α-helix	115-116	2
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	176-185	10	10
α-helix	192-193	2
β-strand	194-200	7	11
α-helix	201-203	3
β-strand	205-211	7	11

Chain I: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	19-25	7	12
β-strand	33-34	2	4
β-strand	35-38	4	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	85-86	2	13
β-strand	89-90	2	4
α-helix	96	1
β-strand	97-98	2	4
β-strand	102-106	5	13
α-helix	107	1
β-strand	111	1	14
β-strand	114-118	5	15
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	15
β-strand	140	1	14
β-strand	147-150	4	16
β-strand	153-154	2	16
β-strand	159-160	2	15
β-strand	163	1	15
α-helix	164-167	4
β-strand	173-182	10	15
α-helix	183-186	4
β-strand	191-195	5	16
β-strand	207-210	4	16

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	17
β-strand	10-14	5	18
β-strand	19-25	7	17
β-strand	33-38	6	18
β-strand	45-49	5	18
β-strand	53-54	2	18
α-helix	55	1
β-strand	62-67	6	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	84-90	7	18
α-helix	96	1
β-strand	97-98	2	18
β-strand	102-107	6	18
β-strand	111	1	19
α-helix	112-113	2
β-strand	114-118	5	20
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	20
β-strand	140	1	19
β-strand	145-150	6	21
β-strand	154	1	21
β-strand	159-163	5	20
α-helix	164-167	4
β-strand	173-182	10	20
α-helix	183-186	4
β-strand	192-197	6	21
β-strand	205-209	5	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Stromal cell-derived factor 1	D, F	protein	61	Homo sapiens	P48061 (AlphaFold model)
hu30D8 Fab heavy chain	E, H	protein	221	Homo sapiens
hu30D8 Fab light chain	I, L	protein	214	Homo sapiens

Sequence of entity 1 (D, F), FASTA

>4LMQ_1 Stromal cell-derived factor 1 (chains D, F)
RCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKALN
K

Sequence of entity 2 (E, H), FASTA

>4LMQ_2 hu30D8 Fab heavy chain (chains E, H)
EVQLVESGGGLVQPGGSLRLSCAASGFSLTVYSVHWVRQAPGKGLEWVGALWGSGGTEYN
SNLKSRFTISRDTSKNTVYLQMNSLRAEDTAVYYCARDQGLNYGSLFDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 3 (I, L), FASTA

>4LMQ_3 hu30D8 Fab light chain (chains I, L)
DIQMTQSPSSLSASVGDRVTITCRASESISYSLSWYQQKPGKAPKLLIYNAVKLESGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCKQYWNTPFTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Development and Preclinical Characterization of a Humanized Antibody Targeting CXCL12. Zhong, C., Wang, J., Li, B. et al. Clin Cancer Res (2013) 19:4433-4445. DOI 10.1158/1078-0432.CCR-13-0943 · PubMed

Other PDB entries of the same protein (UniProt P48061 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3GV3 1.6 Å, CXCL12 (SDF) in trigonal space group
6SHR 1.75 Å, X-ray crystal structure of cell-free protein synthesis (CFPS) produced SDF1-a
4UAI 1.9 Å, Crystal structure of CXCL12 in complex with inhibitor
2J7Z 1.95 Å, Crystal Structure of recombinant Human Stromal Cell-Derived Factor- 1alpha
1QG7 2.0 Å, Stroma cell-derived factor-1ALPHA (sdf-1ALPHA)
2NWG 2.07 Å, Structure of CXCL12:heparin disaccharide complex
1A15 2.2 Å, Sdf-1ALPHA
3HP3 2.2 Å, Crystal structure of CXCL12
9UPV 2.7 Å, Cryo-EM structure of CXCR4 complexed with agonist SDVX1
9UPU 2.8 Å, Cryo-EM strucutre of CXCR4 complexed with agonist SDV1a
8K3Z 2.81 Å, Cryo-EM structure of CXCR4 in complex with CXCL12
8U4O 3.29 Å, Structure of CXCL12-bound CXCR4/Gi complex

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