3D Protein Structures
updated 18/01/01

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Protein Data Bank Home page

PDB ID codes

Each file is stored with a unique four digit code that is a combination of numbers and letters eg 1KEL, 1CD8 etc.

If the file name looks like ***.PDB then the info is stored in a special format that can be read by several graphics programs, such as RasMol, and word processors. You can open these files, read them and save them to your computer for use by RasMol

You can look at any of these molecules is you have installed the Chime plugin
PROTEIN DATA BANK FILES USED IN THIS COURSE
Molecule		Chapter
1KEL	CATALYTIC ANTIBODY (28B4 FAB FRAGMENT COMPLEXED WITH HAPTEN)	4
1CD8	T CELL C0-RECEPTOR (CD8 , N-TERMINAL 114 RESIDUES)	9
2CNA	CONCANAVALIN A
5HMG	INFLUENZA VIRUS HEMAGGLUTININ complexed with Sialic acid	3,17
5HVP	HYDROLASE (ACID PROTEINASE) HIV-1 PROTEASE COMPLEX WITH ACETYL-PEPSTATIN (N*Y5 STRAIN)	4
	HIV Protease & FAb (p93)	4
2HLA	HISTOCOMPATIBILITY ANTIGEN HUMAN CLASS I HISTOCOMPATIBILITY ANTIGEN AW 68.1	7,8
1DLH	HISTOCOMPATIBILITY ANTIGEN HUMAN CLASS II HISTOCOMPATIBILITY PROTEIN COMPLEXED WITH ANTIGENIC PEPTIDE HLA-DR1	7,8
IGG1	HUMAN IGG1 MODEL FROM 2IG2, 1FC2 (HINGE THEORETICAL)	4
1SEB	COMPLEX (MHC II/PEPTIDE/TOXIN) HUMAN MHC CLASS II GLYCOPROTEIN HLA-DR1 COMPLEXED WITH THE BACTERIAL SUPERANTIGEN SEB	7,8
1HUM	CYTOKINE (CHEMOTACTIC) HUMAN MACROPHAGE INFLAMMATORY PROTEIN 1 BETA (HMIP-1B)	1
2IG2	ANTIBODYclass IgG1	4
1HIG	GAMMA INTERFERON:	1
1FYH	Interferon Gamma + Receptor (page 317)	12,17
1FDL	COMPLEX (Fab- Lysozyme)	4,3
1ITA	CYTOKINE INTERLEUKIN 1 ALPHA (THEORETICAL MODEL)	2
1VAB	HISTOCOMPATIBILITY ANTIGEN MHC CLASS I H-2KB COMPLEXED WITH SENDAI VIRUS NUCLEOPROTEIN	7,8
1VAC	COMPLEX (MHC I/PEPTIDE) MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND CHICKEN OVALBUMIN	7,8
1OVA	SERPIN OVALBUMIN (EGG ALBUMIN)(egg albumin)	3
1FAT	LECTIN: PHYTOHEMAGGLUTININ-L
1PLF	PLATELET FACTOR 4	1
1TNR	TUMOR NECROSIS FACTOR RECEPTOR P55 COMPLEXED WITH TUMOR NECROSIS FACTOR-BETA COMPLEX (LYMPHOKINE/RECEPTOR)	1,2
1HEL	LYSOZYME	1,3
1VXC	MYOGLOBIN	3
1MHC	MHC1-ANTIGEN	3,8
1A07	COMPLEX (TCR-ANTIGEN-MHC)	3,9
1AU1	interferon Beta
1A8D	Tetanus toxin	3
1CD1	CD1	8
1CD8	CD8 (page 229)1AKJ	9
1IIE	Invariant chain	8
1A6A	CLIP	8
1FCG	FC Receptor	9
1CDH	CD4 (page 229) 1CDJ	9,10
1RMD	RAG1	11
2CYK	IL4	11,12
1IRL	IL2	11,12
1ILR	IL1 receptor (page 301)	12
2DTB	delta toxin
	CR2 (CD21)	11
	TAPA-1 (cd81)	11
	Cd40	11
	CD45 R CD45o	11
	mouse TCR (page 234)	9
	CD45 PTPase	9
	CD28	9
	B7	9
	Staphylococcal Super antigens	9
	Calnexin	8
	Tapasin	8
	Calreticulin	8
	TAP1 TAP2	8
	Angiotensin II + Fab	3,4
	BSA	3
	KLH	3

Searching the Protein Data Bank

SEARCHLITE

All the data files are stored with a PDB ID. If you know the code this is the fastest way to get the data. Most of us do not remember these codes as there are thousands of different files

The easiest search method is a keyword search of the entire database The keyword,may be the name of molecule, the name of the author who first published the information, the method used or even the PDB ID. The search will return a list of all the files that contain the keyword. The keyword Lysozyme returns a list and a brief description of over 650 files. You select a file and explore it until you found the one that you need. Alternatively you can narrow your search by combining Keywords using boolean logic.

You can get a lot of information quickly by using the Summary Information Page and the Sequence Details Page

Go to the Protein Data Bank Home page , select the SearchLite option and start a search as follows

1: Enter keywords known to relate to the biological macromolecules of interest (eg lysozyme) in the key word window
2: Start the Search Select the "Search" button or "Enter" on your keyboard (PDB is an extremely busy, very large, site, it may take some time for the information to load or you may have to try a few times before accessing the information)
3: Select a file from the list ( use the check off box on the left of the screen)
4; Read the file: Click on the Explore option to activate the Structure Explorer
5: Find the Summary information for the file and answer the following questions

• What is the PDB ID code?
• what is the name of the protein?
• What organism produced the protein?
• How many amino acids are there, and in what sequence?
• How many polypeptide chains? The names of the chains?
• How many atoms are there?
• Are there any additional hetero atoms involved? (what is a hetero atom?)
• Where was the data originally published?
• Who were the authors of the original manuscript?
• What method was used to obtain the 3D coordinates ( X-ray, NMR, Theoretical)

6: Find the Sequence Details section and answer the following questions

• How many polypepide chains are there?
• What is the identification name for each chain?
• How many residues (amino acids or nucleotides) are there
• How many alpha Helices?
• How many Beta Sheets?

7: Download the file to your computer using the Downoad/Display File option

• go to the table entitled Download the Structure File
• select the PDB format with no compression.
• remember the name of the file. the four digit file identification code and the extension.
• remember where you stored the file
• Remember the format of the file

RESOURCES:

Protein Database : database for 3D protein structures

Rasmol Home Page : excellent viewer for those protein structures found in the Brookhaven Protein Database, contains different versions of Rasmol for Windows 3.1, Windows 95 Unix, Macs etc. instructions tips updates etc

Swiss Protein Sequence Database :database for protein sequencesGo to the resources section of the course website and download Protein Database files for B cell receptors and epitopes