Table 2. Position and distribution of Trp residues in structures of known transmembrane barrels.
Position of Trp residued | |||||||
---|---|---|---|---|---|---|---|
S. No.a,b | PDB IDc | Proteina,b | # of β-strandsd,e | # of Trp residues | Membrane interface | Transmembrane | Extra-membrane |
1 | 1P4T | NspA | 10 (8) | 0 | - | - | - |
2 | 2POR | Porin | 22 (16) | 1 | 1 | - | - |
3 | 3QRA | Ail | 9 (8) | 2 | 1 | 1 | - |
4 | 1QJ8 | OmpX | 8 (8) | 2 | 1 | 1 | - |
5 | 2LHF | OprH | 10 (8) | 2 | 2 | - | - |
6 | 3HW9 | OmpF | 25 (16) | 2 | 1 | 1 | - |
7 | 1E54 | Omp32 | 24 (16) | 2 | - | 1 | 1 |
8 | 3DZM | TtoA | 14 (8) | 3 | 1 | - | 2 |
9 | 3FID | LpxR | 17 (12) | 3 | - | 1 | 2 |
10 | 2X27 | OprG | 17 (8) | 4 | 4 | - | - |
11 | 3BRY | TbuX | 27 (14) | 4 | 2 | 2 | - |
12 | 1K24 | OpcA | 15 (10) | 4 | 3 | 1 | - |
13 | 1UYN | NalP | 14 (12) | 4 | 3 | - | 1 |
14 | 1H6S | Porin | 19 (16) | 4 | 3 | 1 | - |
15 | 3EMO | Hia | [6 (4)]x3f | 1 | 1 | - | - |
16 | 4FQE | KdgM | 14 (12) | 3 | 2 | - | 1 |
17 | 1UUN | MspA | [14 (2)]x8f | 4 | 3 | 1 | - |
18 | 3WI4 | PorB | [22 (16)]x3f | 4 | 3 | - | 1 |
19 | 1WP1 | OprM | [13 (4)]x3f | 4 | 2 | - | 2 |
20 | 2LME | YadA | [5 (4)]x3f | 2 | 1 | - | 1 |
aNon-redundant structures were retrieved from PDBTM: Protein Data Bank of Transmembrane Proteins; http://pdbtm.enzim.hu/. Only proteins with a maximum of four Trp residues are listed.
bExamples 15-19 have been classified as porins in PDB; 20 is an anchor protein.
cPDB: RCSB Protein Data Bank; http://www.rcsb.org/pdb.
dInformation derived from both PDBTM and PDB.
eNumbers provided represent the total number of β-strands in the structure and those in brackets represent the total number of transmembrane β-strands.
f[Number of strands in one monomer (Number of transmembrane strands in one monomer)] x Number of monomers.