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CFAD_HUMAN_25_253

Complement factor D [Peptidase S1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CFAD_HUMAN):D: Peptidase S1 (49:51, 66, 67, 69:71, 153:155, 162, 203:208, 222:229, 232)49:51, 66, 67, 69:71, 153:155, 162, 203:208, 222:229, 232

Full PDB list

1bio, 1dfp, 1dic, 1dst, 1dsu, 1fdp, 1hfd, 2xw9, 2xwa, 4cbn, 4cbo, 4d9q, 4d9r, 5fbe, 5fbi, 5fck, 5mt0, 5mt4, 5nar, 5naw, 5nb6, 5nb7, 5nba, 5tca, 5tcc (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
H
4
9
L
5
0
C
5
1
H
6
6
C
6
7
E
6
9
W
1
5
3
G
1
5
4
I
1
5
5
R
1
6
2
S
2
0
3
C
2
0
4
K
2
0
5
G
2
0
6
D
2
0
7
S
2
0
8
V
2
2
2
T
2
2
3
S
2
2
4
G
2
2
5
S
2
2
6
R
2
2
7
C
2
2
9
[1]1bio.a soa9 . . . . . . . . . . . . . . . * . . . . . . .
[1]1dfp.b dfp10 . . . . . . . . . . . . . . . * . . . . . . .
[1]1dic.a dic.o,o12 . . . . . . . . . . . . . . . * . . . . . . .
[1]1dsu.b none . . . . . . . . . . . . . . . . . . . . . . .
[1]2xw9.a none . . . . . . . . . . . . . . . A . . . . . . .
[1]4d9q.a none . . . . . . . . . . . . . . . . . . . . . . .
[1]5fbe.a 5w533 . . . . . . . . . . . . . . . . . . . . . . .
[1]5fbi.a 5wd23 . . . . . . . . . . . . . . . . . . . . . . .
[1]5fck.a 5wc34 . . . . . - . . . . . . . . . . . . . . . . .
[1]5mt0.a qjs25 . . . . . . . . . . . . . . . . . . . . . . .
[1]5mt4.a m7o20 . . . . . . . . . . . . . . . . . . . . . . .
[1]5nar.a 8rw34 . . . . . . . . . . . . . . . . . . . . . . .
[1]5naw.a 8rz35 . . . . . . . . . . . . . . . . . . . . . . .
[1]5nb6.a 8s235 . . . . . . . . . . . . . . . . . . . . . . .
[1]5nb7.a 8nq31 . . . . . . . . . . . . . . . . . . . . . . .
[1]5nba.a 8s535 . . . . . . . . . . . . . . . . . . . . . . .
[1]5tca.b j5530 . . . . . . . . . . . . . . . . . . . . . . .
[1]5tcc.d j5627 . . . . . . . . . . . . . . . . . . . . . . .
[2]1dst.a none . . . . . . . . . . . . . . . . . S W . . . .
[3]4cbo.b none . . . . . . . . . . . . . . . . . . . . . A .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1
H
4
9
L
5
0
C
5
1
H
6
6
C
6
7
E
6
9
D
7
0
A
7
1
W
1
5
3
G
1
5
4
I
1
5
5
R
1
6
2
S
2
0
3
C
2
0
4
K
2
0
5
G
2
0
6
D
2
0
7
S
2
0
8
V
2
2
2
T
2
2
3
S
2
2
4
G
2
2
5
S
2
2
6
R
2
2
7
V
2
2
8
C
2
2
9
R
2
3
2
[1]1bio.a . . . . . . * . . . . * . . . . . * . . . . . . . . .
[1]1dfp.b . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]1dic.a . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]1dsu.b . . . . * . . . . . . * . . * . . * . . . . . . . . .
[1]2xw9.a . . . . . . * . . . . * . . . . . A . . . . . . . . .
[1]4d9q.a . . . . . . * . . . . . . . . . . * . . . . . . . . .
[1]5fbe.a . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]5fbi.a . . . . . . . . . . . * . . * . . * . . . . . . . . .
[1]5fck.a . . . . . - - - . . . . . . . . . . . . . . . . . . .
[1]5mt0.a . . . . . . . . . . . . . . * . . * . . . . . . . . .
[1]5mt4.a . . . . . . . . . . . . . . * . . * . . . . . . . . .
[1]5nar.a . . . . . . - - . . . . . . . . . * . . . . . . . . .
[1]5naw.a . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5nb6.a . . . . . . - - . . . . . . . . . . . . . . . . . . .
[1]5nb7.a . . . . . * . . . . . . . . . . . . . . . . . . . . .
[1]5nba.a . . . . . . - - . . . . . . . . . * . . . . . . . . .
[1]5tca.b . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5tcc.d . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]1dst.a . . . . . . * . . . . * . . * . . * . S W * * . . . .
[3]4cbo.b . . . * . * . . . . . . . . . . . * . . . * * A . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1bio.a:soa
1dfp.b:dfp
1dic.a:dic.o,o
1dsu.b is apo
2xw9.a is apo
4d9q.a is apo
5fbe.a:5w5
5fbi.a:5wd
5fck.a:5wc
5mt0.a:qjs
5mt4.a:m7o
5nar.a:8rw
5naw.a:8rz
5nb6.a:8s2
5nb7.a:8nq
5nba.a:8s5
5tca.b:j55
5tcc.d:j56
1dst.a is apo
4cbo.b is apo
[1] 1bio.a
0.8
0.8 0.9 - - - 3.0 0.3 3.3 4.4 2.1 2.8 2.9 2.8 2.8 2.9 3.0 2.9 - -
[1] 1dfp.b 0.6
0.6
0.6 - - - 0.5 0.1 0.7 0.5 0.2 0.4 0.4 0.5 0.6 0.5 0.4 0.2 - -
[1] 1dic.a 0.6 0.8
0.8
- - - 0.1 0.2 0.1 0.7 0 0.1 0.3 0.1 0.1 0.2 0.2 0.2 - -
[1] 1dsu.b 0.6 0.9 0.7
-
- - 3.3 1.0 2.3 2.4 1.8 2.8 3.9 3.0 2.0 4.2 1.6 1.7 - -
[1] 2xw9.a 0.1 0.3 0.4 -
-
- 3.0 0.5 3.4 3.0 1.7 3.1 2.9 3.1 3.4 3.0 3.5 3.2 - -
[1] 4d9q.a 0.6 0.9 0.6 - -
-
0.6 0 0.8 2.8 1.5 0.9 0.8 1.5 1.0 0.8 1.4 1.4 - -
[1] 5fbe.a 0.6 0.8 0.7 - - -
0.1
0.1 0.2 0.4 0.1 0.1 0.1 0.1 0.4 0.2 0.4 0.4 - -
[1] 5fbi.a 0.6 0.8 0.9 - - - 3.3
0
3.4 3.4 2.7 3.1 3.2 3.1 3.8 3.2 3.8 3.4 - -
[1] 5fck.a 0.1 0.6 0.2 - - - 0.2 0.2
0
0.3 0.1 0.2 0.1 0.3 0.1 0.1 0.1 0 - -
[1] 5mt0.a 0.8 0.8 1.3 - - - 1.1 1.1 1.5
0.1
0.2 1.0 1.5 1.2 1.1 1.3 0.9 1.0 - -
[1] 5mt4.a 0.6 0.9 0.9 - - - 0.8 1.1 1.1 0.7
0.1
0.9 1.3 1.1 0.7 1.4 0.8 0.5 - -
[1] 5nar.a 0.7 0.9 0.8 - - - 0 0 0.3 0.3 0.1
0
0.2 0.1 0 0 0.1 0.1 - -
[1] 5naw.a 0.1 0.5 0.3 - - - 0 0.1 0.2 0.4 0.1 0
0
0 0.3 0 0.3 0.4 - -
[1] 5nb6.a 0.2 0.5 0.6 - - - 0.1 0 0.3 0.4 0.2 0 0.1
0
0.2 0 0.2 0.2 - -
[1] 5nb7.a 0.2 0.7 0.2 - - - 0.2 0.2 0 2.1 0.5 0.1 0.1 0.3
0
0 0 0 - -
[1] 5nba.a 0.7 0.9 0.8 - - - 0 0.1 0.4 0.2 0.1 0 0.2 0.2 0.2
0.1
0.2 0.1 - -
[1] 5tca.b 0.2 0.8 0.5 - - - 0.8 0 0.1 0.7 0.4 0.5 0.6 0.6 0.1 0.6
0
0 - -
[1] 5tcc.d 0.1 0.7 0.3 - - - 0.4 0.1 0.2 1.7 0.7 0.5 0.7 0.3 0.1 0.7 0
0
- -
[2] 1dst.a 3.4 3.7 4.3 - - - 7.3 4.0 7.0 4.2 2.5 7.5 8.0 8.0 7.2 7.5 7.5 5.9
-
-
[3] 4cbo.b 4.9 4.3 5.1 - - - 7.1 6.5 7.3 3.2 2.8 7.4 8.4 7.5 6.9 8.0 7.2 6.0 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 clusters)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1bio.a
1dfp.b
1dic.a
1dsu.b
2xw9.a
4d9q.a
5fbe.a
5fbi.a
5fck.a
5mt0.a
5mt4.a
5nar.a
5naw.a
5nb6.a
5nb7.a
5nba.a
5tca.b
5tcc.d
1dst.a
4cbo.b
[1] 1bio.a
0
.17 .15 .15 .08 .12 .16 .10 .17 .18 .16 .17 .17 .19 .22 .17 .16 .19 .30 .50
[1] 1dfp.b .17
0
.05 .15 .15 .10 .04 .15 .04 .07 .10 .05 .05 .06 .08 .04 .03 .06 .35 .39
[1] 1dic.a .15 .05
0
.16 .14 .09 .03 .16 .03 .08 .09 .04 .04 .05 .08 .04 .05 .07 .36 .37
[1] 1dsu.b .15 .15 .16
0
.11 .23 .15 .08 .17 .11 .09 .16 .17 .18 .21 .16 .16 .18 .36 .49
[1] 2xw9.a .08 .15 .14 .11
0
.19 .15 .06 .15 .15 .12 .16 .13 .15 .20 .16 .14 .17 .33 .49
[1] 4d9q.a .12 .10 .09 .23 .19
0
.10 .22 .11 .15 .16 .11 .12 .13 .16 .10 .11 .15 .30 .45
[1] 5fbe.a .16 .04 .03 .15 .15 .10
0
.13 .02 .07 .09 .01 .03 .03 .08 .01 .03 .08 .38 .37
[1] 5fbi.a .10 .15 .16 .08 .06 .22 .13
0
.15 .10 .11 .15 .15 .15 .20 .15 .13 .18 .33 .47
[1] 5fck.a .17 .04 .03 .17 .15 .11 .02 .15
0
.08 .11 .03 .03 .03 .05 .02 .02 .07 .36 .37
[1] 5mt0.a .18 .07 .08 .11 .15 .15 .07 .10 .08
0
.04 .08 .09 .08 .13 .07 .07 .10 .33 .39
[1] 5mt4.a .16 .10 .09 .09 .12 .16 .09 .11 .11 .04
0
.10 .10 .12 .16 .10 .10 .12 .32 .43
[1] 5nar.a .17 .05 .04 .16 .16 .11 .01 .15 .03 .08 .10
0
.03 .02 .08 .01 .05 .08 .39 .37
[1] 5naw.a .17 .05 .04 .17 .13 .12 .03 .15 .03 .09 .10 .03
0
.02 .08 .03 .05 .08 .38 .37
[1] 5nb6.a .19 .06 .05 .18 .15 .13 .03 .15 .03 .08 .12 .02 .02
0
.08 .03 .04 .09 .38 .38
[1] 5nb7.a .22 .08 .08 .21 .20 .16 .08 .20 .05 .13 .16 .08 .08 .08
0
.08 .08 .05 .42 .32
[1] 5nba.a .17 .04 .04 .16 .16 .10 .01 .15 .02 .07 .10 .01 .03 .03 .08
0
.04 .08 .38 .37
[1] 5tca.b .16 .03 .05 .16 .14 .11 .03 .13 .02 .07 .10 .05 .05 .04 .08 .04
0
.06 .35 .38
[1] 5tcc.d .19 .06 .07 .18 .17 .15 .08 .18 .07 .10 .12 .08 .08 .09 .05 .08 .06
0
.38 .35
[2] 1dst.a .30 .35 .36 .36 .33 .30 .38 .33 .36 .33 .32 .39 .38 .38 .42 .38 .35 .38
0
.37
[3] 4cbo.b .50 .39 .37 .49 .49 .45 .37 .47 .37 .39 .43 .37 .37 .38 .32 .37 .38 .35 .37
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1bio.a
1dfp.b
1dic.a
1dsu.b
2xw9.a
4d9q.a
5fbe.a
5fbi.a
5fck.a
5mt0.a
5mt4.a
5nar.a
5naw.a
5nb6.a
5nb7.a
5nba.a
5tca.b
5tcc.d
1dst.a
4cbo.b
[1] 1bio.a
0
0.8 0.7 1.0 0.7 0.8 0.8 0.8 0.3 0.8 0.6 0.6 0.7 0.5 0.7 0.4 0.8 0.9 2.3 2.1
[1] 1dfp.b 0.8
0
0.7 1.1 0.9 1.0 0.7 0.7 0.6 0.7 0.6 0.8 0.7 0.7 0.8 0.7 0.7 1.0 2.3 2.1
[1] 1dic.a 0.7 0.7
0
1.1 0.8 0.7 0.8 0.8 0.6 0.9 0.7 0.6 0.7 0.6 0.7 0.6 0.9 1.0 2.3 2.2
[1] 1dsu.b 1.0 1.1 1.1
0
1.4 1.0 1.3 1.3 0.7 1.2 1.1 0.8 1.3 0.8 1.4 0.8 1.2 1.5 2.4 2.3
[1] 2xw9.a 0.7 0.9 0.8 1.4
0
1.0 0.9 0.9 0.4 1.0 0.8 0.6 0.7 0.5 0.8 0.5 1.0 1.0 2.5 2.2
[1] 4d9q.a 0.8 1.0 0.7 1.0 1.0
0
1.1 1.1 0.8 1.2 1.0 0.8 1.0 0.8 1.0 0.8 1.1 1.1 2.2 2.1
[1] 5fbe.a 0.8 0.7 0.8 1.3 0.9 1.1
0
0.2 0.3 0.6 0.6 0.5 0.5 0.4 0.7 0.3 0.7 1.0 2.4 2.1
[1] 5fbi.a 0.8 0.7 0.8 1.3 0.9 1.1 0.2
0
0.3 0.6 0.6 0.5 0.5 0.4 0.7 0.3 0.7 0.9 2.5 2.1
[1] 5fck.a 0.3 0.6 0.6 0.7 0.4 0.8 0.3 0.3
0
0.4 0.5 0.4 0.3 0.4 0.4 0.3 0.4 0.5 2.5 1.9
[1] 5mt0.a 0.8 0.7 0.9 1.2 1.0 1.2 0.6 0.6 0.4
0
0.5 0.8 0.7 0.7 0.9 0.7 0.8 1.1 2.4 2.2
[1] 5mt4.a 0.6 0.6 0.7 1.1 0.8 1.0 0.6 0.6 0.5 0.5
0
0.6 0.6 0.5 0.7 0.6 0.6 0.9 2.4 2.1
[1] 5nar.a 0.6 0.8 0.6 0.8 0.6 0.8 0.5 0.5 0.4 0.8 0.6
0
0.5 0.3 0.5 0.3 0.6 0.7 2.5 2.0
[1] 5naw.a 0.7 0.7 0.7 1.3 0.7 1.0 0.5 0.5 0.3 0.7 0.6 0.5
0
0.4 0.4 0.3 0.5 0.7 2.4 2.1
[1] 5nb6.a 0.5 0.7 0.6 0.8 0.5 0.8 0.4 0.4 0.4 0.7 0.5 0.3 0.4
0
0.4 0.3 0.5 0.6 2.5 2.0
[1] 5nb7.a 0.7 0.8 0.7 1.4 0.8 1.0 0.7 0.7 0.4 0.9 0.7 0.5 0.4 0.4
0
0.4 0.6 0.7 2.4 2.0
[1] 5nba.a 0.4 0.7 0.6 0.8 0.5 0.8 0.3 0.3 0.3 0.7 0.6 0.3 0.3 0.3 0.4
0
0.5 0.6 2.5 2.0
[1] 5tca.b 0.8 0.7 0.9 1.2 1.0 1.1 0.7 0.7 0.4 0.8 0.6 0.6 0.5 0.5 0.6 0.5
0
0.6 2.5 2.1
[1] 5tcc.d 0.9 1.0 1.0 1.5 1.0 1.1 1.0 0.9 0.5 1.1 0.9 0.7 0.7 0.6 0.7 0.6 0.6
0
2.5 2.1
[2] 1dst.a 2.3 2.3 2.3 2.4 2.5 2.2 2.4 2.5 2.5 2.4 2.4 2.5 2.4 2.5 2.4 2.5 2.5 2.5
0
1.9
[3] 4cbo.b 2.1 2.1 2.2 2.3 2.2 2.1 2.1 2.1 1.9 2.2 2.1 2.0 2.1 2.0 2.0 2.0 2.1 2.1 1.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1bio.a
1dfp.b
1dic.a
1dsu.b
2xw9.a
4d9q.a
5fbe.a
5fbi.a
5fck.a
5mt0.a
5mt4.a
5nar.a
5naw.a
5nb6.a
5nb7.a
5nba.a
5tca.b
5tcc.d
1dst.a
4cbo.b
[1] 1bio.a
0
1.4 1.3 1.7 0.9 1.4 1.4 1.2 1.0 1.1 0.8 1.2 1.0 1.1 1.3 0.6 1.1 1.3 3.7 2.5
[1] 1dfp.b 1.4
0
1.4 1.9 1.6 1.7 1.4 1.5 1.2 1.2 1.1 1.3 1.2 1.2 1.5 1.0 1.2 1.6 3.8 2.6
[1] 1dic.a 1.3 1.4
0
1.9 1.4 1.6 1.4 1.5 0.9 1.4 1.3 1.0 1.2 1.0 1.1 0.7 1.3 1.5 3.8 2.6
[1] 1dsu.b 1.7 1.9 1.9
0
1.9 1.7 1.9 1.9 1.5 1.7 1.6 1.5 1.8 1.5 2.2 1.1 1.5 2.1 3.8 3.0
[1] 2xw9.a 0.9 1.6 1.4 1.9
0
1.5 1.5 1.4 1.1 1.4 1.2 1.3 1.2 1.3 1.3 0.7 1.3 1.5 3.8 2.7
[1] 4d9q.a 1.4 1.7 1.6 1.7 1.5
0
1.9 1.9 1.4 1.7 1.4 1.4 1.5 1.3 1.8 1.1 1.5 1.7 3.7 2.6
[1] 5fbe.a 1.4 1.4 1.4 1.9 1.5 1.9
0
1.0 0.9 1.0 1.3 0.9 1.2 0.9 1.4 0.5 1.1 1.5 3.9 2.6
[1] 5fbi.a 1.2 1.5 1.5 1.9 1.4 1.9 1.0
0
1.1 1.1 1.3 1.2 1.3 1.3 1.4 0.6 1.1 1.6 3.9 2.8
[1] 5fck.a 1.0 1.2 0.9 1.5 1.1 1.4 0.9 1.1
0
0.8 1.0 0.8 0.7 0.8 0.6 0.5 1.0 1.0 4.0 2.3
[1] 5mt0.a 1.1 1.2 1.4 1.7 1.4 1.7 1.0 1.1 0.8
0
0.8 1.1 1.0 1.1 1.5 0.8 1.1 1.5 3.8 2.7
[1] 5mt4.a 0.8 1.1 1.3 1.6 1.2 1.4 1.3 1.3 1.0 0.8
0
1.1 0.9 1.1 1.4 0.7 1.0 1.3 3.7 2.5
[1] 5nar.a 1.2 1.3 1.0 1.5 1.3 1.4 0.9 1.2 0.8 1.1 1.1
0
1.0 0.4 1.2 0.6 0.9 1.3 3.9 2.4
[1] 5naw.a 1.0 1.2 1.2 1.8 1.2 1.5 1.2 1.3 0.7 1.0 0.9 1.0
0
1.0 1.1 0.4 0.9 1.0 3.8 2.4
[1] 5nb6.a 1.1 1.2 1.0 1.5 1.3 1.3 0.9 1.3 0.8 1.1 1.1 0.4 1.0
0
1.1 0.6 0.8 1.1 4.0 2.4
[1] 5nb7.a 1.3 1.5 1.1 2.2 1.3 1.8 1.4 1.4 0.6 1.5 1.4 1.2 1.1 1.1
0
0.6 0.9 1.0 3.9 2.3
[1] 5nba.a 0.6 1.0 0.7 1.1 0.7 1.1 0.5 0.6 0.5 0.8 0.7 0.6 0.4 0.6 0.6
0
0.7 0.8 3.4 2.2
[1] 5tca.b 1.1 1.2 1.3 1.5 1.3 1.5 1.1 1.1 1.0 1.1 1.0 0.9 0.9 0.8 0.9 0.7
0
0.7 3.9 2.4
[1] 5tcc.d 1.3 1.6 1.5 2.1 1.5 1.7 1.5 1.6 1.0 1.5 1.3 1.3 1.0 1.1 1.0 0.8 0.7
0
4.0 2.3
[2] 1dst.a 3.7 3.8 3.8 3.8 3.8 3.7 3.9 3.9 4.0 3.8 3.7 3.9 3.8 4.0 3.9 3.4 3.9 4.0
0
3.1
[3] 4cbo.b 2.5 2.6 2.6 3.0 2.7 2.6 2.6 2.8 2.3 2.7 2.5 2.4 2.4 2.4 2.3 2.2 2.4 2.3 3.1
0
[Binding site full-atom RMSD matrix]







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