SMTL ID : 7kzm.1

Outer dynein arm bound to doublet microtubules from C. reinhardtii

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-6-1-1-1-1-1-1-1-1-1-1-4-1-1-2-1-2-1-1-mer

Ligands

7 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Covalent)(Non-covalent)

GTP.1: 2 residues within 4Å: Chain A: K.252 Ligands: MG.2 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.252, A:K.252, A:K.252 GTP.5: 18 residues within 4Å: Chain B: G.10, Q.11, A.12, Q.15, D.98, A.100, N.101, G.143, G.144, T.145, G.146, T.179, N.206, Y.224, L.227, N.228 Chain C: K.252 Ligands: MG.4 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:Q.11, B:A.12, B:D.98, B:D.98, B:A.100, B:N.101, B:G.144, B:T.145, B:T.145, B:T.145, B:G.146, B:N.206, B:N.228, B:N.228 pi-Cation interactions: B:Y.224 Salt bridges: C:K.252, C:K.252, C:K.252 GTP.8: 18 residues within 4Å: Chain D: G.10, Q.11, A.12, D.98, A.100, N.101, A.140, G.143, G.144, T.145, G.146, T.179, N.206, Y.224, L.227, N.228 Chain E: K.252 Ligands: MG.7 19 PLIP interactions: 16 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:Q.11, D:A.12, D:D.98, D:D.98, D:A.100, D:N.101, D:G.143, D:G.144, D:T.145, D:T.145, D:G.146, D:N.206, D:N.206, D:N.228, D:N.228 pi-Cation interactions: D:Y.224 Salt bridges: E:K.252, E:K.252, E:K.252 GTP.11: 17 residues within 4Å: Chain F: G.10, Q.11, A.12, Q.15, A.100, N.101, A.140, G.143, G.144, T.145, T.179, N.206, Y.224, L.227, N.228 Chain G: K.252 Ligands: MG.10 17 PLIP interactions: 14 interactions with chain F, 3 interactions with chain G Hydrogen bonds: F:Q.11, F:A.12, F:A.100, F:N.101, F:G.143, F:G.144, F:T.145, F:T.145, F:T.145, F:N.206, F:N.206, F:N.228, F:N.228 pi-Cation interactions: F:Y.224 Salt bridges: G:K.252, G:K.252, G:K.252 GTP.14: 18 residues within 4Å: Chain I: G.10, Q.11, A.12, Q.15, D.98, A.99, N.101, A.140, G.143, G.144, T.145, G.146, N.206, Y.224, N.228 Chain J: L.246, K.252 Ligands: MG.15 20 PLIP interactions: 17 interactions with chain I, 3 interactions with chain J Hydrogen bonds: I:Q.11, I:A.12, I:Q.15, I:D.98, I:N.101, I:G.144, I:T.145, I:T.145, I:T.145, I:G.146, I:N.206, I:N.228, I:N.228, I:N.228 pi-Stacking: I:Y.224, I:Y.224 pi-Cation interactions: I:Y.224 Salt bridges: J:K.252, J:K.252, J:K.252 GTP.18: 20 residues within 4Å: Chain K: G.10, Q.11, A.12, Q.15, E.71, D.98, A.99, A.100, N.101, A.140, G.143, G.144, T.145, G.146, T.179, N.206, Y.224, N.228 Chain L: K.252 Ligands: MG.17 21 PLIP interactions: 18 interactions with chain K, 3 interactions with chain L Hydrogen bonds: K:Q.11, K:A.12, K:D.98, K:A.100, K:N.101, K:G.143, K:G.144, K:T.145, K:T.145, K:G.146, K:E.183, K:N.206, K:N.206, K:N.228, K:N.228 pi-Stacking: K:Y.224, K:Y.224 pi-Cation interactions: K:Y.224 Salt bridges: L:K.252, L:K.252, L:K.252 GTP.21: 18 residues within 4Å: Chain M: G.10, Q.11, A.12, Q.15, A.99, A.100, N.101, A.140, G.143, G.144, T.145, G.146, T.179, N.206, Y.224, N.228 Chain N: K.252 Ligands: MG.20 18 PLIP interactions: 15 interactions with chain M, 3 interactions with chain N Hydrogen bonds: M:Q.11, M:A.12, M:A.99, M:A.100, M:N.101, M:N.101, M:G.144, M:T.145, M:G.146, M:T.179, M:N.206, M:N.206, M:N.228, M:N.228 pi-Cation interactions: M:Y.224 Salt bridges: N:K.252, N:K.252, N:K.252

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: T.145 Ligands: GTP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.145 MG.7: 3 residues within 4Å: Chain D: Q.11, T.145 Ligands: GTP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.145 MG.10: 3 residues within 4Å: Chain F: T.145 Chain G: K.252 Ligands: GTP.11 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain I: D.98 Chain J: K.252 Ligands: GTP.14 No protein-ligand interaction detected (PLIP) MG.17: 5 residues within 4Å: Chain K: Q.11, E.71, D.98 Chain L: K.252 Ligands: GTP.18 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:E.71 MG.20: 2 residues within 4Å: Chain N: K.252 Ligands: GTP.21 No protein-ligand interaction detected (PLIP)

8 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 15 residues within 4Å: Chain A: G.10, Q.11, C.12, Q.15, N.99, G.141, G.142, T.143, G.144, D.177, N.204, L.207, F.222, N.226, I.229 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Q.11, A:C.12, A:N.99, A:G.142, A:T.143, A:G.144, A:N.204, A:N.226, A:N.226, A:N.226 pi-Cation interactions: A:F.222 GDP.6: 14 residues within 4Å: Chain C: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, F.222, N.226 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:Q.11, C:C.12, C:S.138, C:T.143, C:G.144, C:D.177, C:N.204, C:N.226, C:N.226, C:N.226 pi-Stacking: C:F.222, C:F.222 GDP.9: 15 residues within 4Å: Chain E: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, F.222, L.225, N.226 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:Q.11, E:C.12, E:S.138, E:G.141, E:T.143, E:G.144, E:D.177, E:N.204, E:N.226, E:N.226, E:N.226 pi-Cation interactions: E:F.222 GDP.12: 13 residues within 4Å: Chain G: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, N.204, F.222, N.226 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:Q.11, G:C.12, G:S.138, G:G.141, G:G.144, G:N.204, G:N.204, G:N.226, G:N.226 GDP.13: 15 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, F.222, N.226, I.229 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:Q.11, H:C.12, H:S.138, H:G.141, H:G.142, H:G.144, H:N.204, H:N.226, H:N.226, H:N.226 pi-Stacking: H:F.222, H:F.222 pi-Cation interactions: H:F.222 GDP.16: 15 residues within 4Å: Chain J: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, F.222, L.225, N.226 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:Q.11, J:S.138, J:G.142, J:G.144, J:N.204, J:N.226, J:N.226, J:N.226 pi-Stacking: J:F.222, J:F.222 GDP.19: 15 residues within 4Å: Chain L: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, F.222, N.226 Chain M: L.248 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:Q.11, L:C.12, L:S.138, L:G.141, L:G.142, L:G.144, L:D.177, L:N.204, L:N.226, L:N.226, L:N.226 pi-Stacking: L:F.222 pi-Cation interactions: L:F.222 GDP.22: 14 residues within 4Å: Chain N: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, S.145, N.204, F.222, N.226 14 PLIP interactions: 14 interactions with chain N Hydrogen bonds: N:Q.11, N:C.12, N:N.99, N:S.138, N:G.141, N:G.142, N:T.143, N:G.144, N:S.145, N:N.204, N:N.226, N:N.226, N:N.226 pi-Stacking: N:F.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walton, T. et al., Structure of a microtubule-bound axonemal dynein. Nat Commun (2021)

Release Date

2021-01-20

Peptides

Tubulin beta: ACEGHJLN
Tubulin alpha: BDFIKM
Heavy chain alpha: O
Flagellar outer dynein arm heavy chain beta: P
Dynein gamma chain, flagellar outer arm: Q
Dynein, 78 kDa intermediate chain, flagellar outer arm: R
Dynein, 70 kDa intermediate chain, flagellar outer arm: S
Flagellar outer dynein arm light chain 2: T
Dynein 18 kDa light chain, flagellar outer arm: U
Dynein 11 kDa light chain, flagellar outer arm: V
Dynein light chain roadblock LC7a: W
Dynein light chain roadblock LC7b: X
Dynein 8 kDa light chain, flagellar outer arm: YZ01
Dynein light chain 9: 2
Dynein light chain 10: 3
Outer dynein arm-docking complex subunit 1: 46
DC1: 5
Outer dynein arm protein 1: 79
DC2: 8
Outer dynein arm-docking complex protein DC3: a

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A1

C
A3

E
A5

G
A7

H
B1

J
B3

L
B5

N
B7

B
A2

D
A4

F
A6

I
B2

K
B4

M
B6

O
A

P
B

Q
C

R
D

S
E

T
F

U
G

V
H

W
I

X
J

Y
K

Z
L

0
M

1
N

2
O

3
P

4
X

6
X1

5
X0

7
Y

9
Y1

8
Y0

a
Z

Tubulin beta

Tubulin alpha

Heavy chain alpha

Flagellar outer dynein arm heavy chain beta

Dynein gamma chain, flagellar outer arm

Dynein, 78 kDa intermediate chain, flagellar outer arm

Dynein, 70 kDa intermediate chain, flagellar outer arm

Flagellar outer dynein arm light chain 2

Dynein 18 kDa light chain, flagellar outer arm

Dynein 11 kDa light chain, flagellar outer arm

Dynein light chain roadblock LC7a

Dynein light chain roadblock LC7b

Dynein 8 kDa light chain, flagellar outer arm

Dynein light chain 9

Dynein light chain 10

Outer dynein arm-docking complex subunit 1

DC1

Outer dynein arm protein 1

DC2

Outer dynein arm-docking complex protein DC3

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