1AXS: Mature oxy-cope catalytic antibody with hapten

Name: PDB 1AXS: Mature oxy-cope catalytic antibody with hapten
Published: 1998-02-04
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: catalytic antibody

Mature oxy-cope catalytic antibody with hapten. Determined by X-ray diffraction at 2.6 Å resolution. Released 4 Feb 1998.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,887
Mol. weight: 95.94 kDa
Ligands: HOP, CD
Released: 4 Feb 1998

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

Secondary structure: helices and β-sheets

1AXS contains 28 α-helices and 97 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, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	84-90	7	14
α-helix	96	1
β-strand	97-98	2	14
β-strand	99	1	13
β-strand	102-106	5	14
β-strand	111	1	15
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	123-126	4
β-strand	129-139	11	16
β-strand	140	1	15
β-strand	145-150	6	17
β-strand	153-154	2	17
β-strand	159-163	5	16
β-strand	173-182	10	16
α-helix	183-187	5
β-strand	191-197	7	17
β-strand	205-210	6	17

Chain B: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	18
β-strand	11	1	19
β-strand	18-23	6	18
α-helix	29-31	3
β-strand	32-40	9	20
β-strand	44-52	9	20
β-strand	56-59	4	20
α-helix	61-63	3
β-strand	64	1	18
β-strand	67-72	6	18
β-strand	77-82	6	18
α-helix	84-86	3
β-strand	88-97	10	20
β-strand	100	1	20
β-strand	102-103	2	20
β-strand	107-109	3	20
β-strand	110	1	19
α-helix	115-116	2
β-strand	117	1	21
α-helix	118-119	2
β-strand	120-124	5	22
β-strand	135-145	11	22
β-strand	146	1	21
β-strand	151	1	23
β-strand	154	1	23
β-strand	159	1	23
β-strand	163-165	3	22
α-helix	166-168	3
β-strand	169-170	2	22
β-strand	176-185	10	22
β-strand	194-200	7	23
α-helix	201-203	3
β-strand	205-211	7	23
α-helix	212-213	2

Chain H: 8 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	6
α-helix	7-9	3
β-strand	10-12	3	7
β-strand	18-23	6	6
α-helix	29-31	3
β-strand	34-40	7	7
β-strand	44-52	9	7
β-strand	56-59	4	7
α-helix	61-63	3
β-strand	64	1	6
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-94	7	7
β-strand	97	1	8
β-strand	100	1	8
β-strand	102-103	2	7
β-strand	107-111	5	7
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	1	11
β-strand	154	1	12
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	10
β-strand	194-196	3	12
β-strand	199-200	2	11
α-helix	201-203	3
β-strand	205-206	2	11
β-strand	209-211	3	12

Chain L: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	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	99	1	1
β-strand	102-106	5	2
α-helix	107	1
β-strand	111	1	3
β-strand	114-118	5	4
α-helix	119-121	3
β-strand	130-139	10	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
β-strand	159-163	5	4
β-strand	173-181	9	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
Oxy-cope catalytic antibody	A, L	protein	211	Homo sapiens	P01834 (AlphaFold model)
Oxy-cope catalytic antibody	B, H	protein	221	Homo sapiens	P01857 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>1AXS_1 OXY-COPE CATALYTIC ANTIBODY (chains A, L)
ELVLTQSPSSMYASLGERVTITCKASQDINSYLNWFQQKPGKSPKTLIYRTNRLVDGVPS
RFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPYTFGSGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Sequence of entity 2 (B, H), FASTA

>1AXS_2 OXY-COPE CATALYTIC ANTIBODY (chains B, H)
QVQLLESGAELMKPGASVKISCKATGYTFSSFWIEWVKQRPGHGLEWIGEILPGSGGTHY
NEKFKGKATFTADKSSNTAYMQLSSLTSEDSAVYYCARGHSYYFYDGDYWGQGTSVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Ligands and cofactors

ID	Name	Formula	Copies
HOP	(1S,2S,5S)2-(4-glutaridylbenzyl)-5-phenyl-1-cyclohexanol	C23 H27 N O4	2
CD	Cadmium ion	Cd	8

Primary citation

The interplay between binding energy and catalysis in the evolution of a catalytic antibody. Ulrich, H.D., Mundorff, E., Santarsiero, B.D. et al. Nature (1997) 389:271-275. DOI 10.1038/38470 · PubMed

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

5EWI 1.6 Å, Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing…
1NGZ 1.6 Å, Chimeric Germline Fab 7g12-apo
6N35 1.75 Å, Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement
4XMP 1.78 Å, Crystal structure of broadly and potently neutralizing antibody VRC08 in complex with…
1N0X 1.8 Å, Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a…
3VH8 1.8 Å, KIR3DL1 in complex with HLA-B*5701
3X12 1.8 Å, Crystal structure of HLA-B*57:01.I80N
6B9Z 1.82 Å, Trastuzumab Fab v3
2VXQ 1.9 Å, Crystal structure of the major grass pollen allergen Phl p 2 in complex with its…
3D85 1.9 Å, Crystal structure of IL-23 in complex with neutralizing FAB
6BAH 1.9 Å, Trastuzumab Fab v3 with 5-diphenyl meditope variant
6DCV 1.9 Å, Crystal structure of human anti-tau antibody CBTAU-27.1

Browse structure collections

About this viewer

MolViewer shows 1AXS 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.