SMTL ID : 6wsl.1

Cryo-EM structure of VASH1-SVBP bound to microtubules

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-mer

Ligands

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

GTP.1: 20 residues within 4Å: Chain A: Q.11, A.12, Q.15, D.69, E.71, D.98, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228 Chain B: K.252 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:Q.15, A:E.71, A:E.71, A:E.71, A:N.101, A:S.140, A:T.145, A:G.146, A:E.183, A:N.206, A:N.228, A:N.228, A:N.228 pi-Cation interactions: A:Y.224 Salt bridges: B:K.252, B:K.252, B:K.252 GTP.3: 20 residues within 4Å: Chain E: G.10, Q.11, A.12, Q.15, D.69, E.71, D.98, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, N.206, Y.224, L.227, N.228 Chain F: K.252 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:A.12, E:D.69, E:E.71, E:E.71, E:N.101, E:N.101, E:S.140, E:G.142, E:T.145, E:G.146, E:N.206, E:N.228, E:N.228 pi-Cation interactions: E:Y.224 Salt bridges: F:K.252, F:K.252

2 x G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Covalent)

G2P.2: 15 residues within 4Å: Chain B: Q.11, C.12, E.69, A.97, N.99, S.138, G.141, G.142, T.143, G.144, V.169, E.181, N.204, Y.222, N.226 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:E.69, B:E.69, B:N.99, B:S.138, B:G.142, B:T.143, B:T.143, B:T.143, B:G.144, B:T.178, B:T.178, B:E.181, B:E.181, B:N.204, B:N.226, B:N.226, B:N.226 pi-Stacking: B:Y.222 G2P.4: 15 residues within 4Å: Chain F: Q.11, C.12, I.16, E.69, A.97, N.99, S.138, G.141, G.142, T.143, G.144, E.181, N.204, Y.222, N.226 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:Q.11, F:C.12, F:E.69, F:E.69, F:E.69, F:S.138, F:G.142, F:T.143, F:T.143, F:G.144, F:E.181, F:E.181, F:N.204, F:N.226 pi-Stacking: F:Y.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, F. et al., Cryo-EM structure of VASH1-SVBP bound to microtubules. Elife (2020)

Release Date

2020-08-26

Peptides

Tubulin alpha-1A chain: AE
Tubulin beta-3 chain: BF
Tubulinyl-Tyr carboxypeptidase 1: CG
Small vasohibin-binding protein: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

Tubulin alpha-1A chain

Tubulin beta-3 chain

Tubulinyl-Tyr carboxypeptidase 1

Small vasohibin-binding protein

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