2GSI: Murine Fab

Crystal Structure of a Murine Fab in Complex with an 11 Residue Peptide Derived from Staphylococcal Nuclease. Determined by X-ray diffraction at 2.81 Å resolution. Released 16 May 2006.

Method: X-ray diffraction
Resolution: 2.81 Å
Organism: Mus musculus
Chains: 12
Atoms: 13,426
Mol. weight: 194.53 kDa
Released: 16 May 2006

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

Secondary structure: helices and β-sheets

2GSI contains 66 α-helices and 182 β-strands across 12 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: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	1
β-strand	10-14	5	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	102-107	6	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-155	3	5
β-strand	159-163	5	4
α-helix	164-166	3
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	191-197	7	5
α-helix	204	1
β-strand	205-210	6	5

Chain B: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
β-strand	10-12	3	7
β-strand	18-25	8	6
β-strand	33-39	7	7
α-helix	44	1
β-strand	45-52	8	7
β-strand	56-59	4	7
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-96	9	7
β-strand	97-98	2	8
β-strand	100E-103	4	7
β-strand	104	1	6
β-strand	107-111	5	7
β-strand	117	1	9
β-strand	120-124	5	10
β-strand	137-147	11	10
β-strand	148	1	9
β-strand	153-157	4	11
α-helix	162-164	3
β-strand	166	1	11
β-strand	171-173	3	10
α-helix	174-176	3
β-strand	177-179	3	10
β-strand	184-194	11	10
β-strand	206-212	6	11
α-helix	213-215	3
β-strand	217-222	6	11

Chain C: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-25	7	12
β-strand	33-38	6	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	84-90	7	13
α-helix	96	1
β-strand	97-98	2	13
β-strand	102-107	6	13
β-strand	111	1	14
α-helix	112-113	2
β-strand	114-118	5	15
α-helix	119-121	3
α-helix	124-126	3
β-strand	129-139	11	15
β-strand	140	1	14
β-strand	145-150	6	16
β-strand	153-155	3	16
β-strand	159-163	5	15
α-helix	164-167	4
β-strand	173-182	10	15
α-helix	183-186	4
β-strand	191-197	7	16
α-helix	204	1
β-strand	205-210	6	16

Chain D: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	17
β-strand	10-12	3	18
β-strand	18-24	7	17
α-helix	29-31	3
β-strand	33-40	8	18
β-strand	44-52	9	18
β-strand	56-59	4	18
β-strand	67-72	6	17
β-strand	77-82	6	17
α-helix	84-86	3
β-strand	88-96	9	18
β-strand	97	1	19
β-strand	100E-103	4	18
β-strand	104	1	17
β-strand	107-111	5	18
β-strand	117	1	20
α-helix	118-119	2
β-strand	120-124	5	21
β-strand	137-147	11	21
β-strand	148	1	20
β-strand	153-157	4	22
α-helix	162-164	3
β-strand	166	1	22
β-strand	171-173	3	21
α-helix	174-176	3
β-strand	177-179	3	21
β-strand	184-194	11	21
β-strand	205-212	7	22
α-helix	213-215	3
β-strand	217-223	7	22

Chain E: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	23
β-strand	10-14	5	24
β-strand	19-25	7	23
β-strand	33-38	6	24
β-strand	45-49	5	24
β-strand	53-54	2	24
α-helix	55	1
β-strand	62-67	6	23
β-strand	70-75	6	23
α-helix	80-82	3
β-strand	84-90	7	24
α-helix	96	1
β-strand	97-98	2	24
β-strand	102-107	6	24
β-strand	111	1	25
α-helix	112-113	2
β-strand	114-118	5	26
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	26
β-strand	140	1	25
β-strand	144-150	7	27
β-strand	153-155	3	27
β-strand	159-163	5	26
α-helix	164-167	4
β-strand	173-182	10	26
α-helix	183-186	4
β-strand	191-198	8	27
β-strand	205-210	6	27

Chain F: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	28
α-helix	7	1
β-strand	10-12	3	29
β-strand	18-25	8	28
α-helix	29-31	3
β-strand	33-39	7	29
β-strand	45-52	8	29
β-strand	56-59	4	29
α-helix	61-63	3
β-strand	67-72	6	28
β-strand	77-82	6	28
α-helix	84-86	3
β-strand	88-96	9	29
β-strand	97-98	2	30
β-strand	100E-103	4	29
β-strand	104	1	28
β-strand	107-111	5	29
α-helix	117-119	3
β-strand	120-124	5	31
β-strand	137-147	11	31
β-strand	153-157	4	11
α-helix	162-164	3
β-strand	166	1	11
β-strand	171-173	3	31
α-helix	174-176	3
β-strand	177-178	2	31
β-strand	185-194	10	31
β-strand	206-212	6	11
α-helix	213-215	3
β-strand	217-222	6	11
α-helix	223-227	3

Chain G: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	32
β-strand	10-14	5	33
β-strand	19-25	7	32
β-strand	33-38	6	33
α-helix	43-44	2
β-strand	45-49	5	33
β-strand	53-54	2	33
α-helix	55	1
β-strand	63-67	5	32
β-strand	70-75	6	32
α-helix	78-79	2
α-helix	80-82	3
β-strand	84-90	7	33
α-helix	96	1
β-strand	97-98	2	33
β-strand	99	1	32
β-strand	102-107	6	33
β-strand	111	1	34
α-helix	112-113	2
β-strand	114-118	5	35
α-helix	119-121	3
α-helix	124-126	3
β-strand	129-139	11	35
β-strand	140	1	34
β-strand	145-150	6	36
β-strand	153-154	2	36
β-strand	159-163	5	35
α-helix	165-167	3
β-strand	173-182	10	35
α-helix	183-186	4
β-strand	191-197	7	36
β-strand	205-210	6	36

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	37
β-strand	10-12	3	38
β-strand	18-25	8	37
α-helix	29-31	3
β-strand	33-40	8	38
β-strand	44-52	9	38
β-strand	56-59	4	38
α-helix	61-63	3
β-strand	64	1	37
β-strand	67-72	6	37
α-helix	73-75	3
β-strand	77-82	6	37
α-helix	84-86	3
β-strand	88-95	8	38
β-strand	97-98	2	39
β-strand	102-103	2	38
β-strand	107-111	5	38
β-strand	117	1	40
α-helix	118-119	2
β-strand	120-124	5	41
β-strand	138-147	10	41
β-strand	148	1	40
β-strand	153-157	4	42
α-helix	162-164	3
β-strand	171-173	3	41
α-helix	174-176	3
β-strand	177-179	3	41
β-strand	184-193	10	41
α-helix	195-198	3
β-strand	206-212	6	42
β-strand	217-222	6	42

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin (kappa) light chain	A, C, E, G	protein	215	Mus musculus
Immunoglobulin (gamma) heavy chain (VH + CH1 fragment)	B, D, F, H	protein	221	Mus musculus	Q6PF95 (AlphaFold model)
Thermonuclease	W, X, Y, Z	protein	11		P00644 (AlphaFold model)

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

>2GSI_1 Immunoglobulin (kappa) light chain (chains A, C, E, G)
DIVLTQSPASLAVSLGQPATISCGASKSVRTSGYSYMDWNQQKPGQPPRRLIYLVSNLES
GVPARFSGSGSGTDFTLNIHPVEEEDAATYYCSHIRELPRSSGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR

Sequence of entity 2 (B, D, F, H), FASTA

>2GSI_2 Immunoglobulin (gamma) heavy chain (VH + CH1 fragment) (chains B, D, F, H)
VQLQQSGAELVRSGASVKLSCTASGFNIKDYYMYWVKLRPEQGLEWIGWIDPENGDTEYV
PTFQGKVTMTADTSSNTAYLQLSSLTSEDTAVYYCNAGVITMMGYQAMDYWGQGTTVTTS
SAKTTPPSVYPLAPGTAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQS
DLYTLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPR

Sequence of entity 3 (W, X, Y, Z), FASTA

>2GSI_3 Thermonuclease (chains W, X, Y, Z)
TKHPKKGVEKY

Primary citation

Crystal Structure of a Murine Fab in Complex with an 11 Residue Peptide Derived from Staphylococcal Nuclease. Armstrong, A.A., Amzel, L.M. To be published.

Other PDB entries of the same protein (UniProt Q6PF95 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1EJO 2.3 Å, FAB fragment of neutralising monoclonal antibody 4C4 complexed with G-H loop from fmdv.
1JN6 2.7 Å, Crystal Structure of Fab-Estradiol Complexes
1XGY 2.71 Å, Crystal Structure of Anti-Meta I Rhodopsin Fab Fragment K42-41L
2A6K 3.0 Å, Crystal Structure Analysis of the germline antibody 36-65 Fab in complex with the…

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