TABLE 2.
Statistics about CCR5 three-dimensional models
| CCR5 models |
|||||||
|---|---|---|---|---|---|---|---|
| CCR5_Rho | CCR5_Ops | CCR5_AdrB2 | CCR5_AA2a | CCR5_mix | CCR5_CXCR4_peptide | CCR5_CXCR4_small | |
| Template | Bovine rhodopsin (1u19) | Bovine opsin (3dqb) | Human β2-adrenergic receptor (2rh1) | Human A2A adenosine receptor (3eml) | TM1.4–7 from bovine rhodopsin (1f88), ab initio TM2.3 | Human chemokine receptor type 4 (3oe0) | Human chemokine receptor type 4 (3odu) |
| Modeled domain | 7TMa | 7TMa | 7TMa | 7TMa | 7TMa, N terminus, ECL1, ECL2, and ECL3b | Ser-17 to Ala-298 | A: Pro-19 to Cys-323; B: Cys-20 to Gln-313 |
| Sequence conservation in the 7TM | |||||||
| Identityc | 23.3% | 23.3% | 25.4% | 22.2% | 23.3% | 35.4% | 35.4% |
| Similarityc | 46.0% | 46.0% | 48.1% | 47.1% | 46.0% | 62.4% | 62.4% |
| Geometryd in the 7TM | |||||||
| Main chain | 92.1 | 93.3 | 96.9 | 97.0 | 93.1 | 95.0 | 93.7//92.5 |
| Side chain | 13.3/9.0 | 10.7/8.1 | 11.6/8.3 | 12.1/9.3 | 12.7/12.4 | 10.4/8.7 | 9.7/6.9//11.4/13.9 |
| 7TM cavity volumee | 1083 Å3 | 1092 Å3 | 1089 Å3 | 834 Å3 | 975 Å3 | 942 Å3 | 846//990 Å3 |
a The 7TM is defined as in Table 1.
b The modeled extracellular domains are a tripeptide of the N-terminal domain (N terminus: Val-25 to Gln-27), the first extracellular loop (ECL1, Trp-94 to Gly-97), part of the second extracellular loop (ECL2, Phe-166, Thr-177 to Ser-179, and Trp-109), and part of the third extracellular loop (ECL3, Leu-256 to Gln-261, and Asn-273 to Asp-276).
c Data are between the target and template 7TM sequences. Two residues are noted similar if the score of substitution pair in a blosum62 matrix is positive or null.
d Percent residues in most favored regions of Ramachandran plot (top) and standard deviation from ideal values of χ1 and χ2 angles in degrees (bottom) were computed using Procheck version 3.5 (49).
e The volume of the 7TM cavity (without loops) was measured using the in-house program VolSite.