2DQU: Immunoglobulin 6D9

Crystal form II: high resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog. Determined by X-ray diffraction at 1.7 Å resolution. Released 20 Jun 2006.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,679
Mol. weight: 48.98 kDa
Ligands: CPD
Released: 20 Jun 2006

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

Secondary structure: helices and β-sheets

2DQU contains 14 α-helices and 47 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: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	2
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	45-51	7	2
β-strand	57-59	3	2
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	2
β-strand	100K-103	4	2
β-strand	107-111	5	2
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	9
β-strand	127	1	10
β-strand	135-145	11	9
β-strand	146	1	8
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	9
α-helix	166-168	3
β-strand	169-171	3	9
β-strand	174-184	11	9
β-strand	194-199	6	11
α-helix	200-202	3
β-strand	204-209	6	11
β-strand	213	1	10

Chain L: 7 helices, 23 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	27C	1	3
β-strand	31	1	3
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	4
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-155	3	6
β-strand	159-163	5	5
β-strand	173-182	10	5
α-helix	183-186	4
β-strand	191-197	7	6
β-strand	205-210	6	6
α-helix	211-213	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin 6D9	L	protein	219	Mus musculus	A2NHM3 (AlphaFold model)
Immunoglobulin 6D9	H	protein	224	Mus musculus	P18527 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>2DQU_1 IMMUNOGLOBULIN 6D9 (chains L)
DVLMTQTPLSLPVSLGDQASISCRSSQTIVHSNGDTYLDWFLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPPTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>2DQU_2 IMMUNOGLOBULIN 6D9 (chains H)
EVKLVESGGGLVKPGGSLKLSCAASGFTFSNYAMSWVRQTPEKRLEWVVSISSGGSIYYL
DSVKGRFTVSRDNARNILYLQMTSLRSEDTAMYFCARVSHYDGSRDWYFDVWGAGTSVTV
SSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQ
SDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Ligands and cofactors

ID	Name	Formula	Copies
CPD	[1-(3-dimethylamino-propyl)-3-ethyl-ureido]-[4-(2,2,2-trifluoro-acetylamino)-be…	C28 H36 Cl2 F3 N6 O8 P	1

Primary citation

Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis. Oda, M., Ito, N., Tsumuraya, T. et al. J Mol Biol (2007) 369:198-209. DOI 10.1016/j.jmb.2007.03.023 · PubMed

Other PDB entries of the same protein (UniProt A2NHM3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6PXR 1.56 Å, Anti-TAU BIIB092 FAB with TAU peptide
4TPR 1.6 Å, Structure of Tau5 antibody Fab fragment
4TQE 1.6 Å, Structure of tau peptide in complex with Tau5 antibody Fab fragment
3V4U 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UO1 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
2IPU 1.65 Å, PFA1 Fab fragment complexed with Abeta 1-8 peptide
3V52 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UYR 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
1ZEA 1.78 Å, Structure of the anti-cholera toxin antibody Fab fragment TE33 in complex with a D-peptide
1PZ5 1.8 Å, Structural basis of peptide-carbohydrate mimicry in an antibody combining site
2DQT 1.8 Å, High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and…
1T2Q 1.83 Å, The Crystal Structure of an NNA7 Fab that recognizes an N-type blood group antigen

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