7RGA: NanoCLAMP3:VHH

Crystal structure of nanoCLAMP3:VHH in complex with MTX. Determined by X-ray diffraction at 2.9 Å resolution. Released 25 May 2022.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: synthetic construct
Chains: 7
Atoms: 14,664
Mol. weight: 232 kDa
Ligands: MTX
Released: 25 May 2022

Explore 7RGA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RGA contains 34 α-helices and 159 β-strands across 7 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: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-15	6	1
α-helix	17-20	4
β-strand	29-33	5	1
β-strand	39	1	2
β-strand	41	1	3
β-strand	43	1	3
β-strand	44-62	19	1
β-strand	75-81	7	1
β-strand	88-94	7	1
α-helix	98-99	2
β-strand	103-122	20	1
β-strand	126	1	2
β-strand	131-138	8	1
β-strand	178-181	4	4
β-strand	185-187	3	5
β-strand	192-198	7	4
β-strand	207-213	7	6
β-strand	219-225	7	6
β-strand	232-234	3	6
β-strand	239	1	4
β-strand	242-247	6	4
β-strand	252-257	6	4
α-helix	262-264	3
β-strand	266-273	8	6
α-helix	278-280	3
β-strand	287-288	2	6
β-strand	289	1	4
β-strand	292-294	3	6
β-strand	295-297	3	5

Chain B: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-15	6	7
α-helix	19-21	3
β-strand	29-33	5	7
β-strand	39	1	8
α-helix	40	1
β-strand	44-62	19	7
β-strand	67	1	9
β-strand	75-81	7	7
β-strand	88-94	7	7
α-helix	98-99	2
β-strand	103-122	20	7
β-strand	126	1	8
β-strand	131-138	8	7
β-strand	178-181	4	10
β-strand	184-186	3	11
β-strand	192-198	7	10
β-strand	200	1	9
β-strand	207-213	7	11
α-helix	218-219	2
β-strand	220-225	6	11
β-strand	232-234	3	11
β-strand	242-247	6	10
β-strand	252-257	6	10
α-helix	262-264	3
β-strand	266-273	8	11
α-helix	278-280	3
β-strand	287-288	2	11
β-strand	292-296	5	11

Chain C: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
β-strand	10-15	6	12
α-helix	17-21	5
β-strand	29-33	5	12
β-strand	39	1	13
β-strand	44-62	19	12
β-strand	75-81	7	12
β-strand	87-94	8	12
α-helix	98-99	2
β-strand	103-122	20	12
β-strand	126	1	13
β-strand	131-138	8	12
β-strand	178-181	4	14
β-strand	185-187	3	15
β-strand	192-198	7	14
β-strand	207-213	7	16
β-strand	220-225	6	16
β-strand	232-234	3	16
β-strand	242-247	6	14
β-strand	252-257	6	14
α-helix	262-264	3
β-strand	266-273	8	16
α-helix	277-280	4
β-strand	287-288	2	16
β-strand	292-294	3	16
β-strand	295-297	3	15

Chain D: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	17
β-strand	10-14	5	17
α-helix	17-21	5
β-strand	29-33	5	17
β-strand	39	1	18
α-helix	40	1
β-strand	44-62	19	17
β-strand	75-81	7	17
β-strand	88-94	7	17
β-strand	103-122	20	17
β-strand	126	1	18
β-strand	131-138	8	17
β-strand	178-181	4	19
β-strand	185-187	3	20
β-strand	192-198	7	19
β-strand	207-213	7	21
β-strand	219-225	7	21
β-strand	232-234	3	21
α-helix	236-238	3
β-strand	242-247	6	19
β-strand	252-257	6	19
α-helix	262-264	3
β-strand	266-273	8	21
α-helix	276-279	4
β-strand	287-288	2	21
β-strand	292-294	3	21
β-strand	295-297	3	20

Chain E: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	22
β-strand	10-15	6	22
α-helix	17-20	4
β-strand	29-33	5	22
β-strand	39	1	23
α-helix	40	1
β-strand	44-62	19	22
β-strand	75-81	7	22
β-strand	88-94	7	22
α-helix	98-99	2
β-strand	103-122	20	22
β-strand	126	1	23
β-strand	131-138	8	22
β-strand	178-181	4	24
β-strand	185	1	25
β-strand	191-198	8	24
β-strand	207-213	7	26
β-strand	219-225	7	26
β-strand	232-234	3	26
α-helix	236-238	3
β-strand	242-247	6	24
β-strand	252-258	7	24
α-helix	262-264	3
β-strand	266-273	8	26
α-helix	278-280	3
β-strand	287-288	2	26
β-strand	292-294	3	26
β-strand	295	1	25

Chain F: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	27
β-strand	10-14	5	27
α-helix	17-21	5
β-strand	29-33	5	27
β-strand	39	1	28
β-strand	44-63	20	27
β-strand	76-81	6	27
β-strand	88-92	5	27
α-helix	98-99	2
β-strand	103-122	20	27
β-strand	126	1	28
β-strand	131-138	8	27
β-strand	178-181	4	29
β-strand	185-187	3	30
β-strand	192-198	7	29
β-strand	207-213	7	31
β-strand	220-225	6	31
β-strand	232-234	3	31
β-strand	242-247	6	29
β-strand	252-257	6	29
α-helix	262-264	3
β-strand	266-273	8	31
α-helix	277-280	4
β-strand	287-288	2	31
β-strand	292-294	3	31
β-strand	295-297	3	30

Chain G: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	2	1
β-strand	3-6	4	32
β-strand	10-14	5	32
β-strand	29-33	5	32
β-strand	39	1	33
α-helix	40	1
β-strand	44-62	19	32
β-strand	75-81	7	32
β-strand	88-94	7	32
α-helix	98-99	2
β-strand	103-122	20	32
β-strand	126	1	33
β-strand	131-138	8	32
β-strand	178-181	4	34
β-strand	186-187	2	35
β-strand	191-198	8	34
β-strand	207-213	7	36
β-strand	220-225	6	36
β-strand	232-234	3	36
β-strand	243-247	5	34
β-strand	252-258	7	34
α-helix	262-264	3
β-strand	266-273	8	36
α-helix	278-280	3
β-strand	287-288	2	36
β-strand	292-294	3	36
β-strand	296-297	2	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
nano CLostridial Antibody Mimetic Protein 3 VHH	A, B, C, D, E, F, G	protein	306	synthetic construct	P26831 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G), FASTA

>7RGA_1 nano CLostridial Antibody Mimetic Protein 3 VHH (chains A, B, C, D, E, F, G)
DHHHHHHSNPSLIRSESWHVYDGNEANLLDGDDNTGVWYKRSNGEASLAGEFIGLDLGKE
IKLDGIRFVIGKNGGGSSDKWNKFKLEYSLDNESWTTIKEYDKTGAPAGKDVIEESFETP
ISAKYIRLTNLEPRHVQLTFSEFAIVSDGGSGSGASGSGSGSGSGASGGSSGGSGGSGGG
GSQVQLVESGGGLVQAGGSLRLSCAASRRSSRSWAMAWFRQAPGKEREFVAKISGDGRLT
TYGDSVKGRFTISRDNAEYLVYLQMDSLKPEDTAVYYCAADDNYVTASWRSGPDYWGQGT
QVTVSS

Ligands and cofactors

ID	Name	Formula	Copies
MTX	Methotrexate	C20 H22 N8 O5	7

Water and common crystallization additives (NA) are not listed.

Primary citation

Design of a methotrexate-controlled chemical dimerization system and its use in bio-electronic devices. Guo, Z., Smutok, O., Johnston, W.A. et al. Nat Commun (2021) 12:7137-7137. DOI 10.1038/s41467-021-27184-w · PubMed

Other PDB entries of the same protein (UniProt P26831 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2W1S 1.45 Å, Unique ligand binding specificity of a family 32 Carbohydrate-Binding Module from the Mu…
2OZN 1.6 Å, The Cohesin-Dockerin Complex of NagJ and NagH from Clostridium perfringens
2W1Q 1.6 Å, Unique ligand binding specificity for a family 32 Carbohydrate- Binding Module from the…
2W1U 2.0 Å, A family 32 carbohydrate-binding module, from the Mu toxin produced by Clostridium…
2WDB 2.03 Å, A family 32 carbohydrate-binding module, from the Mu toxin produced by Clostridium…
2JNK Solution structure of a dockerin-containing modular pair from a family 84 glycoside…

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