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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Yin, L."

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Search Summary

This query matches 43 Structures.

Refinements

Structure Determination Methodology

experimental (43)

Scientific Name of Source Organism

	Severe acute respiratory syndrome coronavirus 2 (16)
	Homo sapiens (11)
	Aeropyrum pernix K1 (6)
	Aliarcobacter butzleri (6)
	Agaricales sp. 'Arthromyces ramosus (3)
	Hemitrygon akajei (2)
	Photobacterium phosphoreum (2)
	Pseudomonas sp. PDC86 (2)
	synthetic construct (2)
	Mythimna separata (1)

More...

Taxonomy

	Eukaryota (19)
	Riboviria (17)
	Bacteria (10)
	Archaea (6)
	other sequences (2)

Experimental Method

	X-RAY DIFFRACTION (28)
	ELECTRON MICROSCOPY (14)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (43)

Refinement Resolution (Å)

	1.5 - 2.0 (5)
	2.0 - 2.5 (12)
	2.5 - 3.0 (12)
	3.0 - 3.5 (11)
	3.5 - 4.0 (2)

Release Date

	1995 - 1999 (5)
	2000 - 2004 (2)
	2005 - 2009 (2)
	2010 - 2014 (3)
	2015 - 2019 (3)
	2020 - 2024 (28)

Enzyme Classification Name

	Hydrolases (9)
	Transferases (7)
	Lyases (8)
	Oxidoreductases (3)

Membrane Protein Annotation

	PDBTM (6)
	MemProtMD (5)

Symmetry Type

	Asymmetric (23)
	Cyclic (21)
	Icosahedral (1)

SCOP Classification

	Alpha and beta proteins (a/b) (8)
	All alpha proteins (6)
	All beta proteins (1)

AllSelected

1 to 25 of 43 Structures

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1C8I \| pdb_00001c8i	Download File View File

BINDING MODE OF HYDROXYLAMINE TO ARTHROMYCES RAMOSUS PEROXIDASE

Wariishi, H., Nonaka, D., Johjima, T., Nakamura, N., Naruta, Y., Kubo, K., Fukuyama, K.

(2000) J Biological Chem 275: 32919-32924

Released	2001-01-17
Method	X-RAY DIFFRACTION 2 Å
Organisms	Agaricales sp. 'Arthromyces ramosus
Macromolecule	PROTEIN (PEROXIDASE) (protein)
Unique Ligands	BMA, CA, HEM, HOA
Unique branched monosaccharides	NAG

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1C8N \| pdb_00001c8n	Download File View File

TOBACCO NECROSIS VIRUS

Oda, Y., Fukuyama, K.

(2000) J Mol Biology 300: 153-169

Released	2000-08-30
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	unidentified tobacco necrosis virus
Macromolecule	COAT PROTEIN (protein)
Unique Ligands	CA

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1CG5 \| pdb_00001cg5	Download File View File

DEOXY FORM HEMOGLOBIN FROM DASYATIS AKAJEI

Chong, K.T., Morimoto, H.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1291-1300

Released	1999-04-01
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Hemitrygon akajei
Macromolecule	PROTEIN (HEMOGLOBIN) (protein)
Unique Ligands	HEM

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1CG8 \| pdb_00001cg8	Download File View File

CO Form Hemoglobin from Dasyatis Akajei

Chong, K.T., Morimoto, H.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1291-1300

Released	1999-04-01
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Hemitrygon akajei
Macromolecule	PROTEIN (HEMOGLOBIN) (protein)
Unique Ligands	CMO, HEM

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1CK6 \| pdb_00001ck6	Download File View File

BINDING MODE OF SALICYLHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PEROXIDASE

Fukuyama, K., Itakura, H.

(1999) Biochemistry 38: 12558-12568

Released	1999-12-29
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Agaricales sp. 'Arthromyces ramosus
Macromolecule	PROTEIN (PEROXIDASE) (protein)
Unique Ligands	BMA, CA, HEM, SHA
Unique branched monosaccharides	NAG

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1HSR \| pdb_00001hsr	Download File View File

BINDING MODE OF BENZHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PEROXIDASE

Fukuyama, K., Itakura, H.

(1997) FEBS Lett 412: 107-110

Released	1998-07-01
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Agaricales sp. 'Arthromyces ramosus
Macromolecule	PEROXIDASE (protein)
Unique Ligands	BHO, CA, HEM
Unique branched monosaccharides	NAG

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1HSS \| pdb_00001hss	Download File View File

0.19 ALPHA-AMYLASE INHIBITOR FROM WHEAT

Oda, Y., Fukuyama, K.

(1997) Biochemistry 36: 13503-13511

Released	1998-07-01
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Triticum aestivum
Macromolecule	0.19 ALPHA-AMYLASE INHIBITOR (protein)

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1WKV \| pdb_00001wkv	Download File View File

Crystal structure of O-phosphoserine sulfhydrylase

Oda, Y., Mino, K., Ishikawa, K., Ataka, M.

(2005) J Mol Biology 351: 334-344

Released	2005-06-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Aeropyrum pernix K1
Macromolecule	cysteine synthase (protein)
Unique Ligands	ACT, PLP

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2RPS \| pdb_00002rps	Download File View File

Solution structure of a novel insect chemokine isolated from integument

Kamiya, M., Nakatogawa, S., Oda, Y., Kamijima, T., Aizawa, T., Demura, M., Hayakawa, Y., Kawano, K.

(2009) Curr Biol 19: 779-785

Released	2009-06-16
Method	SOLUTION NMR
Organisms	Mythimna separata
Macromolecule	Chemokine (protein)

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3VSA \| pdb_00003vsa	Download File View File

Crystal Structure of O-phosphoserine sulfhydrylase without acetate

Nakamura, T., Kawai, Y., Kataoka, M., Ishikawa, K.

(2012) J Mol Biology 422: 33-44

Released	2012-05-16
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Protein CysO (protein)
Unique Ligands	MPD, PLP

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3VSC \| pdb_00003vsc	Download File View File

Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Phospho-L-Serine

Nakamura, T., Kawai, Y., Kataoka, M., Ishikawa, K.

(2012) J Mol Biology 422: 33-44

Released	2012-05-16
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Protein CysO (protein)
Unique Ligands	MPD, PLP, SEP

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3VSD \| pdb_00003vsd	Download File View File

Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine

Nakamura, T., Kawai, Y., Kataoka, M., Ishikawa, K.

(2012) J Mol Biology 422: 33-44

Released	2012-05-16
Method	X-RAY DIFFRACTION 2.09 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Protein CysO (protein)
Unique Ligands	MPD, OAS, PLP

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5B36 \| pdb_00005b36	Download File View File

Crystal Structure of the O-Phosphoserine Sulfhydrylase from Aeropyrum pernix Complexed with Cysteine

Nakamura, T., Takeda, E., Kawai, Y., Kataoka, M., Ishikawa, K.

(2016) Extremophiles 20: 733-745

Released	2016-03-16
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Protein CysO (protein)
Unique Ligands	CYS, MPD, PLP

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5B3A \| pdb_00005b3a	Download File View File

Crystal Structure of O-Phoshoserine Sulfhydrylase from Aeropyrum pernix in Complexed with the alpha-Aminoacrylate Intermediate

Nakamura, T., Takeda, E., Kawai, Y., Kataoka, M., Ishikawa, K.

(2016) Extremophiles 20: 733-745

Released	2016-03-16
Method	X-RAY DIFFRACTION 2.14 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Protein CysO (protein)
Unique Ligands	0JO, MPD

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6J6Y \| pdb_00006j6y	Download File View File

FGFR4 D2 - Fab complex

Takahashi, M., Hanzawa, H.

(2019) Mol Cancer Ther 18: 1832-1843

Released	2019-08-07
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Fab Heavy chain (protein) Fab light chain (protein) Fibroblast growth factor receptor 4 (protein)

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7ERU \| pdb_00007eru	Download File View File

Crystal structure of L-histidine decarboxylase (C57S mutant) from Photobacterium phosphoreum

Oda, Y., Nakata, K., Yamaguchi, H., Kashiwagi, T., Miyano, H., Mizukoshi, T.

(2022) J Biochem 171: 31-40

Released	2022-02-16
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Photobacterium phosphoreum
Macromolecule	Histidine decarboxylase (protein)

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7ERV \| pdb_00007erv	Download File View File

Crystal structure of L-histidine decarboxylase (C57S/C101V/C282V mutant) from Photobacterium phosphoreum

Oda, Y., Nakata, K., Yamaguchi, H., Kashiwagi, T., Miyano, H., Mizukoshi, T.

(2022) J Biochem 171: 31-40

Released	2022-02-16
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Photobacterium phosphoreum
Macromolecule	Histidine decarboxylase (protein)
Unique Ligands	IMD

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7KZ8 \| pdb_00007kz8	Download File View File

Crystal structure of substrate-binding protein Aapf from Pseudomonas sp. PDC86

Luo, S., Dadhwal, P., Tong, L.

(2021) Proc Natl Acad Sci U S A 118:

Released	2021-03-17
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pseudomonas sp. PDC86
Macromolecule	Peptide/nickel transport system substrate-binding protein AapF (protein)
Unique Ligands	GOL

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7KZ9 \| pdb_00007kz9	Download File View File

Crystal structure of Pseudomonas sp. PDC86 substrate-binding protein Aapf in complex with a signaling molecule HEHEAA

Luo, S., Dadhwal, P., Tong, L.

(2021) Proc Natl Acad Sci U S A 118:

Released	2021-03-17
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Pseudomonas sp. PDC86
Macromolecule	Peptide/nickel transport system substrate-binding protein AapF (protein)
Unique Ligands	GOL, SO4, XN7

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7XWA \| pdb_00007xwa	Download File View File

Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.4/5 variant spike protein in complex with its receptor ACE2

Suzuki, T., Kimura, K., Hashiguchi, T.

(2022) Cell 185: 3992

Released	2022-09-28
Method	X-RAY DIFFRACTION 3.36 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Processed angiotensin-converting enzyme 2 (protein) Spike protein S1 (protein)
Unique Ligands	NAG, ZN
Unique branched monosaccharides	BMA, MAN, NAG

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7XY8 \| pdb_00007xy8	Download File View File

Crystal structure of antibody Fab fragment in complex with CD147(EMMPIRIN)

Nakamura, K., Amano, M., Yoneda, K., Suzuki, M., Fukuchi, K.

(2022) J Oncol 2022: 3552793-3552793

Released	2022-11-23
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Isoform 2 of Basigin (protein) heavy chain (protein) light chain (protein)

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8GS6 \| pdb_00008gs6	Download File View File

Structure of the SARS-CoV-2 BA.2.75 spike glycoprotein (closed state 1)

Anraku, Y., Tabata-Sasaki, K., Kita, S., Fukuhara, H., Maenaka, K., Hashiguchi, T.

(2022) Cell Host Microbe 30: 1540-1555.e15

Released	2022-10-26
Method	ELECTRON MICROSCOPY 2.86 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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8H9O \| pdb_00008h9o	Download File View File

Crystal structure of voltage-gated sodium channel NavAb N49K mutant in sodium ion condition

Irie, K.

(2023) Nat Commun 14: 4236-4236

Released	2023-07-26
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Aliarcobacter butzleri
Macromolecule	Ion transport protein (protein)
Unique Ligands	1N7, LMT, NA, PX4

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8H9W \| pdb_00008h9w	Download File View File

Crystal structure of voltage-gated sodium channel NavAb N49K mutant in calcium ion condition

Irie, K.

(2023) Nat Commun 14: 4236-4236

Released	2023-07-26
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Aliarcobacter butzleri
Macromolecule	Ion transport protein (protein)
Unique Ligands	1N7, CA, LMT, PX4

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8H9X \| pdb_00008h9x	Download File View File

Crystal structure of voltage-gated sodium channel NavAb N49K/L176Q mutant in sodium ion condition

Irie, K., Oda, Y.

(2023) Nat Commun 14: 4236-4236

Released	2023-07-26
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Aliarcobacter butzleri
Macromolecule	Ion transport protein (protein)
Unique Ligands	1N7, LMT, NA, PX4

1 to 25 of 43 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

1C8I | pdb_00001c8i

1C8N | pdb_00001c8n

1CG5 | pdb_00001cg5

1CG8 | pdb_00001cg8

1CK6 | pdb_00001ck6

1HSR | pdb_00001hsr

1HSS | pdb_00001hss

1WKV | pdb_00001wkv

2RPS | pdb_00002rps

3VSA | pdb_00003vsa

3VSC | pdb_00003vsc

3VSD | pdb_00003vsd

5B36 | pdb_00005b36

5B3A | pdb_00005b3a

6J6Y | pdb_00006j6y

7ERU | pdb_00007eru

7ERV | pdb_00007erv

7KZ8 | pdb_00007kz8

7KZ9 | pdb_00007kz9

7XWA | pdb_00007xwa

7XY8 | pdb_00007xy8

8GS6 | pdb_00008gs6

8H9O | pdb_00008h9o

8H9W | pdb_00008h9w

8H9X | pdb_00008h9x