1D6V: PDB entry 1D6V

Conformation effects in biological catalysis introduced by oxy-cope antibody maturation. Determined by X-ray diffraction at 2.0 Å resolution. Released 9 Feb 2000.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Mus musculus, Homo sapiens
Chains: 2
Atoms: 3,486
Mol. weight: 47.96 kDa
Ligands: HOP, CD
Released: 9 Feb 2000

Explore 1D6V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1D6V contains 19 α-helices and 44 β-strands across 2 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 H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
α-helix	7-9	3
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	32-39	8	7
β-strand	45-52	8	7
β-strand	56-59	4	7
β-strand	64	1	6
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-97	10	7
β-strand	102-103	2	7
β-strand	107-111	5	7
α-helix	114-116	3
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	9
β-strand	135-145	11	9
β-strand	146	1	8
β-strand	151-154	4	10
α-helix	155-157	3
β-strand	159	1	10
β-strand	163-165	3	9
α-helix	166-168	3
β-strand	169-170	2	9
β-strand	176-185	10	9
α-helix	188-191	4
β-strand	195-200	6	10
α-helix	201-203	3
β-strand	205-210	6	10

Chain L: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-149	5	5
α-helix	153	1
β-strand	154	1	5
α-helix	155	1
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	191-197	7	5
β-strand	205-210	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chimeric germline precursor of oxy-cope catalytic antibody az-28 (light chain)	L	protein	211	Mus musculus, Homo sapiens	P01834 (AlphaFold model)
Chimeric germline precursor of oxy-cope catalytic antibody az-28 (heavy chain)	H	protein	221	Mus musculus, Homo sapiens	P01857 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1D6V_1 CHIMERIC GERMLINE PRECURSOR OF OXY-COPE CATALYTIC ANTIBODY AZ-28 (LIGHT CHAIN) (chains L)
DIKMTQSPSSMYASLGERVTITCKASQDINSYLSWFQQKPGKSPKTLIYRANRLVDGVPS
RFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPYTFGSGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Sequence of entity 2 (H), FASTA

>1D6V_2 CHIMERIC GERMLINE PRECURSOR OF OXY-COPE CATALYTIC ANTIBODY AZ-28 (HEAVY CHAIN) (chains H)
QVQLQQSGAELMKPGASVKISCKATGYTFSSYWIEWVKQRPGHGLEWIGEILPGSGSTNY
NEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCARGHSYYFYDGDYWGQGTSVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Ligands and cofactors

ID	Name	Formula	Copies
HOP	(1S,2S,5S)2-(4-glutaridylbenzyl)-5-phenyl-1-cyclohexanol	C23 H27 N O4	1
CD	Cadmium ion	Cd	4

Primary citation

Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearrangement. Mundorff, E.C., Hanson, M.A., Varvak, A. et al. Biochemistry (2000) 39:627-632. DOI 10.1021/bi9924314 · PubMed

Other PDB entries of the same protein (UniProt P01834 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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3D85 1.9 Å, Crystal structure of IL-23 in complex with neutralizing FAB
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6DCV 1.9 Å, Crystal structure of human anti-tau antibody CBTAU-27.1

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