MMDB

A structure from the NCBI in the cn3 format.

Displaying 1 - 50 of 172

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Structure Description

 Toll Like Receptor bound to Lipotechoic acid

Collection
PDB ID
3A7B
Structure Type
Structure file
mmdb_3A7B.cn3
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Structure Description

A DNA

Collection
PDB ID
371D
Structure Type

One of the things that drives me crazy on occasion is nomenclature. Well, maybe not just nomenclature, it's really the continual changes in the nomenclature, and the time it takes for those changes to ripple through various databases and get reconciled with other kinds of information. And the realization that ...

Science Blog
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Structure Description

Aidan Cytochrome C oxidase.  This file contains half of the complete structure.

PDB ID
5B1A
Structure Type

What’s the first you think about when you see a spider? Running away? Danger? Fairies? Spiderman? Do you wonder if spider silk is really strong enough to stop a train, like they showed in Spiderman 2? Whatever your thoughts, you’re probably not thinking about 3D printing in space. Yet, the ...

Science Blog
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Structure Description

A wild-type form of alpha amylase from Bacillus licheniformis.

Collection
PDB ID
1BLI
Structure Type
Structure file
1BL1.cn3
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Structure Description

A heat tolerant form of alpha amylase, engineered from Bacillus lichenformis and Bacillus amyloliquifaciens.

Collection
PDB ID
1E3Z
Structure Type
Structure file
1E3Z.cn3
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Structure Description

Alpha amylase with maltose from Bacillus sp.707.  Maltose is produced when alpha amylase digests starch. Select the first five glucose monomers (GLC) to highlight maltose.  

Collection
PDB ID
2D3L
Structure Type
Structure file
2D3L.cn3
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Structure Description

Amino Acid Receptor / Ion Channel

Crystal Structure of Glun1a/glun2b Nmda Receptor Ion Channel

Collection
PDB ID
4PE5
Structure Type
Structure file
mmdb_4PE5.cn3
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Structure Description

An antifreeze protein from an Antarctic bacterium (Marinomonas primoryensis).

Collection
PDB ID
3P4G
Structure Type
Structure file
3P4G.cn3
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Structure Description

Fab portions of antibodies bound to Ebola virus

Collection
PDB ID
5FHC
Structure Type
Structure file
mmdb_5FHC.cn3
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Structure Description

Fab portions of antibodies bound to the HIV prefusion trimer

Collection
PDB ID
5I8H
Structure Type
Structure file
mmdb_5I8H.cn3
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Structure Description

B DNA

Collection
PDB ID
1BNA
Structure Type
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Structure Description

A beta amylase from Bacillus cereus.  This enzyme works best at pH 6.5.

Collection
PDB ID
1VEM
Structure Type
Structure file
1VEM.cn3
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Structure Description

A beta amylase from Bacillus cereus engineered to work at a lower pH (4.6).  The tyrosine at position 164 has been changed to glutamic acid (Y164e)

Collection
PDB ID
1VEN
Structure Type
Structure file
1VEN.cn3
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Structure Description

A beta amylase from Bacillus cereus engineered to work at a lower pH (4.6).  The tyrosine at position 164 has been changed to phenylalanine (Y164f)

Collection
PDB ID
1VEO
Structure Type
Structure file
1VEO.cn3
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Structure Description

Boris' Cytochrome C oxidase.  This file contains half of the complete structure.

PDB ID
3ABK
Structure Type
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Structure Description

BRCA1 carboxyl terminal end, contains BRCT repeats and the CtIP binding domain.  M1775

Collection
PDB ID
1JNX
Structure Type
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Structure Description

BRCA1 carboxyl terminal end, BRCT repeats.  Contains the CtIP binding domain and M1775r mutation.

Collection
PDB ID
1N5O
Structure Type
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Structure Description

Capsaicin receptor, also called the TrpVI Ion channel.

PDB ID
3J5P
Structure Type
Structure file
3J5P.cn3
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Structure Description

Capsaicin receptor bound to spider toxin.

PDB ID
3J5Q
Structure Type
Structure file
3J5Q.cn3
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Structure Description

Carboxypeptidase A bound to the metallocarboxypeptidase inhibitor from the potato.  A glycine has been cleaved from the end of the inhibitor and appears in the complex.

Collection
PDB ID
4CPA
Structure Type
Structure file
4CPA.cn3.gz
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Structure Description

Cas1 and Cas2, nucleases from E. coli that chop up and store viral DNA.

Collection
PDB ID
4P6I
Structure Type
Structure file
mmdb_4P6I.cn3
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Structure Description

Cas3, a nuclease from Thermobifida fusca that attacks viral DNA.

Collection
PDB ID
4QQW
Structure Type
Structure file
mmdb_4QQW.cn3
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Structure Description

Cas9 from Streptococcus pyogenes with CRISPR RNA bound to double-stranded target DNA.

Collection
PDB ID
4UN3
Structure Type
Structure file
mmdb_4UN3.cn3
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Structure Description

Cas9 from Streptococcus pyogenes Cas9 bound to guide RNA and a single-stranded DNA target.

Collection
PDB ID
4OO8
Structure Type
Structure file
mmdb_4OO8.cn3
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Structure Description

Cas9 from Streptococcus pyogenes with CRISPR RNA about to cut to double-stranded target DNA.

Collection
PDB ID
5F9R
Structure Type
Structure file
mmdb_5F9R.cn3
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Structure Description

A Cascade CRISPR surveillance complex from E. coli

Collection
PDB ID
4TVX
Structure Type
Structure file
mmdb_4TVX.cn3
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Structure Description

Another structure of the Cascade CRISPR surveillance complex from E. coli

Collection
PDB ID
4U7U
Structure Type
Structure file
mmdb_4U7U.cn3
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Structure Description

CCR5 chemokine receptor

Collection
PDB ID
4MBS
Structure Type
Structure file
mmdb_4MBS.cn3
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Structure Description

Antibodies bound to CD28

Collection
PDB ID
1YJD
Structure Type
Structure file
mmdb_1YJD.cn3
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Structure Description

CD40 bound to CD154 (CD40 ligand)

Collection
PDB ID
3QD6
Structure Type
Structure file
mmdb_3QD6.cn3
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Structure Description

CD40 ligand bound to Fab fragments

PDB ID
1I9R
Structure Type
Structure file
mmdb_1I9R.cn3
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Structure Description

CD8 bound to Class I MHC and peptide

PDB ID
1AKJ
Structure Type
Structure file
mmdb_1AKJ.cn3
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Structure Description

CD8 bound to Class I MHC and peptide

Collection
PDB ID
3QZW
Structure Type
Structure file
mmdb_3QZW.cn3
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Structure Description

Charlotte's Cytochrome C oxidase.  This file contains half of the complete structure.

PDB ID
2ZXW
Structure Type
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Structure Description

Class I HLA bound to peptide

PDB ID
5C09
Structure Type
Structure file
mmdb_5C09.cn3
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Structure Description

Co-stimulatory complex - T cell receptor, CD80 and CTL 4

Collection
PDB ID
1I8L
Structure Type
Structure file
mmdb_1I8L.cn3
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Structure Description

Co-stimulatory complex - T cell receptor, CD86 and CTL 4

Collection
PDB ID
1I85
Structure Type
Structure file
mmdb_1I85.cn3

Over 2600 genetic diseases have been found where a change in a single gene is linked to the disease. One of the questions we might ask is how those mutations change the shape and possibly the function of a protein? If the structures of the mutant and wild type (normal) ...

Science Blog
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Structure Description

Complement C9 membrane attack complex, alpha carbons

Collection
PDB ID
5FMW
Structure Type
Structure file
mmdb_5FMW.cn3
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Structure Description

A venom protein made by the carnivorous cone snail.

Collection
PDB ID
1IXT
Structure Type
Structure file
1IXT.cn3.gz
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Structure Description

E. coli CRISPR complex with guide RNA bound to target DNA.

Collection
PDB ID
4QYZ
Structure Type
Structure file
mmdb_4QYZ.cn3
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Structure Description

This protein is a snake toxin with phospholipase activity.  

This structure shows hydrogens because it was obtained by NMR.

PDB ID
3R0L
Structure Type
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Structure Description

CTLA-4 dimer

Collection
PDB ID
3OSK
Structure Type
Structure file
mmdb_3OSK.cn3
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Structure Description

A short chain of double-stranded DNA.  Hydrogens are not shown because this structure was obtained through X-ray diffraction.

Collection
PDB ID
2BNA
Structure Type
Structure file
2BNA.cn3
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Structure Description

A short chain of double-stranded DNA showing hydrogens. Hydrogens are present because this structure was solved by NMR.

Collection
PDB ID
1NAJ
Structure Type

On pinene and inhibiting enzymes. People of a certain age may remember a series of really funny commercials featuring Euell Gibbons and his famous question about whether you've ever eaten a pine tree. " Some parts are edible" said Euell. Perhaps some parts are, but other pine tree products aren't ...

Science Blog
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Structure Description

A double-stranded DNA molecule. Hydrogens are not seen because this structure was solved by X-ray diffraction.

Collection
PDB ID
2BNA
Structure Type
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Structure Description

A double-stranded DNA molecule. Hydrogens are not seen because this structure was solved by X-ray diffraction.

Collection
PDB ID
2BNA
Structure Type
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