SMTL ID : 7kzo.1

Outer dynein arm docking complex bound to doublet microtubules from C. reinhardtii

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-6-1-2-2-1-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
Dynein gamma chain, flagellar outer arm: O
Outer dynein arm-docking complex subunit 1: PR
Outer dynein arm protein 1: QS
Outer dynein arm-docking complex protein DC3: T

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
C

P
X

R
X1

Q
Y

S
Y1

T
Z

Tubulin beta

Tubulin alpha

Dynein gamma chain, flagellar outer arm

Outer dynein arm-docking complex subunit 1

Outer dynein arm protein 1

Outer dynein arm-docking complex protein DC3

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