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234,785 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Chemical ID(s) = IND

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Search Summary

This query matches 22 Structures.

Refinements

Structure Determination Methodology

experimental (22)

Scientific Name of Source Organism

	Pseudomonas putida (3)
	Homo sapiens (2)
	Paenibacillus sp. A11-2 (2)
	Anopheles gambiae (1)
	Aspergillus flavus (1)
	Canavalia lineata (1)
	Methylophaga aminisulfidivorans (1)
	Mus musculus (1)
	Plasmodium falciparum 3D7 (1)
	Rhodococcus sp. NCIMB 12038 (1)

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Taxonomy

	Bacteria (13)
	Eukaryota (7)
	Archaea (1)
	Duplodnaviria (1)
	other sequences (1)

Experimental Method

X-RAY DIFFRACTION (22)

Polymer Entity Type

Protein (22)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (9)
	2.0 - 2.5 (7)
	2.5 - 3.0 (4)
	3.0 - 3.5 (1)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (3)
	2005 - 2009 (3)
	2010 - 2014 (5)
	2015 - 2019 (3)
	2020 - 2024 (6)
	2025 - 2029 (1)

Enzyme Classification Name

	Oxidoreductases (8)
	Transferases (3)
	Hydrolases (2)
	Lyases (1)

Membrane Protein Annotation

	OPM (2)
	MemProtMD (1)
	PDBTM (1)
	mpstruc (1)

Symmetry Type

	Cyclic (15)
	Asymmetric (7)
	Dihedral (5)

SCOP Classification

	Alpha and beta proteins (a+b) (5)
	All beta proteins (6)
	All alpha proteins (2)
	Alpha and beta proteins (a/b) (2)
	Artifacts (1)
	Membrane and cell surface proteins and peptides (1)

AllSelected

1 to 22 of 22 Structures

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185L \| pdb_0000185l	Download File View File

SPECIFICITY OF LIGAND BINDING IN A BURIED NON-POLAR CAVITY OF T4 LYSOZYME: LINKAGE OF DYNAMICS AND STRUCTURAL PLASTICITY

Morton, A., Matthews, B.W.

(1995) Biochemistry 34: 8576-8588

Released	1995-07-10
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Tequatrovirus T4
Macromolecule	T4 LYSOZYME (protein)
Unique Ligands	CL, HED, IND

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1EG9 \| pdb_00001eg9	Download File View File

NAPHTHALENE 1,2-DIOXYGENASE WITH INDOLE BOUND IN THE ACTIVE SITE.

Carredano, E., Karlsson, A., Kauppi, B., Choudhury, D., Parales, R.E., Parales, J.V., Lee, K., Gibson, D.T., Eklund, H., Ramaswamy, S.

(2000) J Mol Biology 296: 701-712

Released	2000-05-24
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Pseudomonas putida
Macromolecule	PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT) (protein) PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT) (protein)
Unique Ligands	FE, FES, IND, SO4

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1L4H \| pdb_00001l4h	Download File View File

Crystal Structure of CobT complexed with indole and nicotinate mononucleotide

Cheong, C.-G., Escalante-Semerena, J., Rayment, I.

(2002) J Biological Chem 277: 41120-41127

Released	2002-09-07
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Salmonella enterica
Macromolecule	Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (protein)
Unique Ligands	IND, NCN

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1O7N \| pdb_00001o7n	Download File View File

NAPHTHALENE 1,2-DIOXYGENASE, TERNARY COMPLEX WITH DIOXYGEN AND INDOLE

Karlsson, A., Parales, J.V., Parales, R.E., Gibson, D.T., Eklund, H., Ramaswamy, S.

(2003) Science 299: 1039

Released	2003-02-20
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Pseudomonas putida
Macromolecule	NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT (protein) NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT (protein)
Unique Ligands	EDO, FE, FES, IND, OXY, SO4

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1UUV \| pdb_00001uuv	Download File View File

NAPHTHALENE 1,2-DIOXYGENASE WITH NITRIC OXIDE AND INDOLE BOUND IN THE ACTIVE SITE.

Karlsson, A., Parales, J.V., Parales, R.E., Gibson, D.T., Eklund, H., Ramaswamy, S.

(2005) J Biol Inorg Chem 10: 483

Released	2005-02-09
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Pseudomonas putida
Macromolecule	NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT (protein) NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT (protein)
Unique Ligands	EDO, FE, FES, IND, NO, SO4

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2B24 \| pdb_00002b24	Download File View File

Crystal structure of naphthalene 1,2-dioxygenase from Rhodococcus sp. bound to indole

Gakhar, L., Malik, Z.A., Allen, C.C., Lipscomb, D.A., Larkin, M.J., Ramaswamy, S.

(2005) J Bacteriol 187: 7222-7231

Released	2005-10-04
Method	X-RAY DIFFRACTION 3 Å
Organisms	Rhodococcus sp. NCIMB 12038
Macromolecule	naphthalene dioxygenase large subunit (protein) naphthalene dioxygenase small subunit (protein)
Unique Ligands	FE, FES, IND

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2P85 \| pdb_00002p85	Download File View File

Structure of Human Lung Cytochrome P450 2A13 with indole bound in two alternate conformations

Scott, E.E., Stout, C.D.

(2007) J Biological Chem 282: 17306-17313

Released	2007-04-10
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Homo sapiens
Macromolecule	Cytochrome P450 2A13 (protein)
Unique Ligands	HEM, IND

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2XVJ \| pdb_00002xvj	Download File View File

Crystal structure of the mutant bacterial flavin containing monooxygenase in complex with indole

Cho, H.J., Kang, B.S.

(2011) J Struct Biol 175: 39

Released	2011-05-04
Method	X-RAY DIFFRACTION 2.48 Å
Organisms	Methylophaga aminisulfidivorans
Macromolecule	FLAVIN-CONTAINING MONOOXYGENASE (protein)
Unique Ligands	FAD, IND, MES, NO3, OXY

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3Q8I \| pdb_00003q8i	Download File View File

Crystal structure of Anopheles Gambiae odorant binding protein 4 in complex with indole

Davrazou, F., Dong, E., Murphy, E.J., Jones, D.N.M.

To be published

Released	2011-08-03
Method	X-RAY DIFFRACTION 2 Å
Organisms	Anopheles gambiae
Macromolecule	Odorant binding protein (protein)
Unique Ligands	IND, PO4

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3SNM \| pdb_00003snm	Download File View File

Crystal structure of a lectin from Canavalia maritima seeds complexed with Indole-3-Acetic Acid

Delatorre, P., Silva-Filho, J.C., Nobrega, R.B., Rocha, B.C., Cavada, B.S., Gadelha, C.A.A., Santi-Gadelha, T., Alencar, K.L.

(2013) Biochimie 95: 1697-1703

Released	2012-08-01
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Canavalia lineata
Macromolecule	Concanavalin-A (protein)
Unique Ligands	CA, IAC, IND, MN

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4EAN \| pdb_00004ean	Download File View File

1.75A resolution structure of indole bound beta-glycosidase (W33G) from sulfolobus solfataricus

Lovell, S., Battaile, K.P., Deckert, K., Brunner, L.C., Budiardjo, S.J., Karanicolas, J.

(2012) J Am Chem Soc 134: 10055-10060

Released	2012-06-13
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	Beta-galactosidase (protein)
Unique Ligands	CL, IND, MPD

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4UUJ \| pdb_00004uuj	Download File View File

POTASSIUM CHANNEL KCSA-FAB WITH TETRAHEXYLAMMONIUM

Lenaeus, M.J., Burdette, D., Wagner, T., Focia, P.J., Gross, A.

(2014) Biochemistry 53: 5365

Released	2014-08-27
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Mus musculus Streptomyces lividans
Macromolecule	ANTIBODY FAB FRAGMENT HEAVY CHAIN (protein) ANTIBODY FAB FRAGMENT LIGHT CHAIN (protein) VOLTAGE-GATED POTASSIUM CHANNEL KCSA (protein)
Unique Ligands	CO, DGA, F09, IND, K, PO4, XA7

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5LVW \| pdb_00005lvw	Download File View File

XiaF (FADH2) from Streptomyces sp.

Kugel, S., Baunach, M., Baer, P., Ishida-Ito, M., Sundaram, S., Xu, Z., Groll, M., Hertweck, C.

(2017) Nat Commun 8: 15804-15804

Released	2017-06-28
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Streptomyces sp.
Macromolecule	XiaF protein (protein)
Unique Ligands	FAD, IND, SO4

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5XDC \| pdb_00005xdc	Download File View File

Crystal structure of Indole-bound TdsC from Paenibacillus sp. A11-2

Hino, T., Hamamoto, H., Ohshiro, T., Nagano, S.

(2017) J Biological Chem 292: 15804-15813

Released	2017-08-09
Method	X-RAY DIFFRACTION 1.5785 Å
Organisms	Paenibacillus sp. A11-2
Macromolecule	Thermophilic dibenzothiophene desulfurization enzyme C (protein)
Unique Ligands	GOL, IND, SO4

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5XDD \| pdb_00005xdd	Download File View File

Crystal structure of tertiary complex of TdsC from Paenibacillus sp. A11-2 with FMN and Indole

Hino, T., Hamamoto, H., Ohshiro, T., Nagano, S.

(2017) J Biological Chem 292: 15804-15813

Released	2017-08-09
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Paenibacillus sp. A11-2
Macromolecule	Thermophilic dibenzothiophene desulfurization enzyme C (protein)
Unique Ligands	FMN, GOL, IND, SO4

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7WGI \| pdb_00007wgi	Download File View File

Crystal structure of AflSQS from Aspergillus flavus

Shang, N., Liu, W.D., Chen, C.C., Guo, R.T.

(2022) ACS Omega 7: 22601-22612

Released	2022-11-09
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Aspergillus flavus
Macromolecule	Squalene synthase (protein)
Unique Ligands	IND, PO4

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7Z94 \| pdb_00007z94	Download File View File

Crystal structure of Variovorax paradoxus indole monooxygenase (VpIndA1) in complex with indole

Kratky, J., Weisse, R., Strater, N.

(2023) Angew Chem Int Ed Engl 62: e202300657-e202300657

Released	2023-02-22
Method	X-RAY DIFFRACTION 1.74 Å
Organisms	Variovorax paradoxus EPS
Macromolecule	Putative dehydrogenase/oxygenase subunit (Flavoprotein) (protein)
Unique Ligands	DMS, FAD, IND, NA, SO4

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7ZHI \| pdb_00007zhi	Download File View File

Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor indole

Wang, C., Zhang, B.

(2022) J Am Chem Soc 144: 19070-19077

Released	2022-08-24
Method	X-RAY DIFFRACTION 2.946 Å
Organisms	Plasmodium falciparum 3D7
Macromolecule	Aspartate carbamoyltransferase (protein)
Unique Ligands	IND, SO4

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8B05 \| pdb_00008b05	Download File View File

TRYPTOPHAN SYNTHASE - Cryo-trapping by the spitrobot crystal plunger after 20 sec

Mehrabi, P., Sung, S., von Stetten, D., Prester, A., Hatton, C.E., Kleine-Dopke, S., Berkes, A., Gore, G., Leimkohl, J.P., Schikora, H., Kollewe, M., Rohde, H., Wilmanns, M., Tellkamp, F., Schulz, E.C.

(2023) Nat Commun 14: 2365-2365

Released	2023-05-03
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	Tryptophan synthase alpha chain (protein) Tryptophan synthase beta chain (protein)
Unique Ligands	CL, CS, IND, PLS

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8GAD \| pdb_00008gad	Download File View File

Crystal structure of a high affinity PD-L1 binder

Yang, W., Almo, S.C., Baker, D., Ghosh, A.

(2024) bioRxiv

Released	2024-08-21
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	synthetic construct
Macromolecule	PD-L1 binder (protein)
Unique Ligands	IND

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8R2S \| pdb_00008r2s	Download File View File

Heme-dependent l-tyrosine hydroxylase (TyrH) from Streptomyces sclerotialus: fourfold mutant

Carraretto, D., Mattevi, A.

(2024) ChemCatChem

Released	2024-12-18
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Streptomyces sclerotialus
Macromolecule	L-tyrosine 3-hydroxylase (protein)
Unique Ligands	ACT, HEM, IND, PEG

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9KND \| pdb_00009knd	Download File View File

Crystal structure of human ERRg LBD in complex with indole

Xu, T., Wang, N., Liu, J.

(2025) Acta Pharmacol Sin

Released	2025-04-16
Method	X-RAY DIFFRACTION 1.52 Å
Organisms	Homo sapiens
Macromolecule	Estrogen-related receptor gamma (protein) Nuclear receptor-interacting protein 1 (protein)
Unique Ligands	IND

1 to 22 of 22 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

185L | pdb_0000185l

1EG9 | pdb_00001eg9

1L4H | pdb_00001l4h

1O7N | pdb_00001o7n

1UUV | pdb_00001uuv

2B24 | pdb_00002b24

2P85 | pdb_00002p85

2XVJ | pdb_00002xvj

3Q8I | pdb_00003q8i

3SNM | pdb_00003snm

4EAN | pdb_00004ean

4UUJ | pdb_00004uuj

5LVW | pdb_00005lvw

5XDC | pdb_00005xdc

5XDD | pdb_00005xdd

7WGI | pdb_00007wgi

7Z94 | pdb_00007z94

7ZHI | pdb_00007zhi

8B05 | pdb_00008b05

8GAD | pdb_00008gad

8R2S | pdb_00008r2s

9KND | pdb_00009knd