SMTL ID : 7d73.1

Cryo-EM structure of GMPPA/GMPPB complex bound to GTP (State I)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-8-mer

Ligands

2 x GDD: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE(Covalent)(Non-covalent)

GDD.1: 27 residues within 4Å: Chain A: L.7, I.8, G.9, K.13, I.56, G.57, F.58, E.85, L.89, G.90, T.91, N.114, A.115, D.116, V.117, Y.152, G.153, Y.167, E.169, K.170, N.180, C.181, Y.184, E.223, W.245, Q.247, K.249 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:I.8, A:I.56, A:G.90, A:T.91, A:N.114, A:A.115, A:D.116, A:D.116, A:G.153, A:E.169, A:N.180, A:N.180, A:Y.184, A:E.223, A:Q.247 Salt bridges: A:K.13, A:E.85, A:K.170, A:K.170, A:K.249, A:K.249, A:K.249 GDD.4: 26 residues within 4Å: Chain D: L.7, I.8, G.9, K.13, I.56, G.57, F.58, E.85, L.89, G.90, T.91, N.114, A.115, D.116, V.117, Y.152, G.153, Y.167, E.169, N.180, C.181, Y.184, E.223, W.245, Q.247, K.249 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:I.8, D:K.13, D:I.56, D:L.89, D:G.90, D:N.114, D:A.115, D:D.116, D:D.116, D:G.153, D:E.169, D:E.169, D:N.180, D:N.180, D:C.181, D:Q.247 Salt bridges: D:E.85, D:K.249, D:K.249, D:K.249

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

GTP.2: 16 residues within 4Å: Chain B: L.7, I.8, K.13, I.56, G.57, F.58, E.85, L.89, G.90, N.114, A.115, D.116, E.169, K.170, E.223, Q.224 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:L.7, B:I.56, B:L.89, B:G.90, B:A.115, B:D.116, B:D.116, B:D.116, B:E.169, B:Q.224 Salt bridges: B:K.13, B:E.85, B:K.170 GTP.3: 18 residues within 4Å: Chain C: L.6, V.7, G.8, G.9, G.11, T.12, R.13, K.23, A.52, V.53, S.54, E.80, P.83, L.84, G.85, N.108, S.109, D.110 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:G.8, C:G.9, C:G.9, C:G.11, C:T.12, C:R.13, C:R.13, C:A.52, C:A.52, C:S.54, C:G.85, C:S.109 Salt bridges: C:R.13, C:K.23, C:K.23, C:K.23, C:E.80 GTP.5: 18 residues within 4Å: Chain E: L.7, I.8, G.9, K.13, I.56, G.57, F.58, E.85, L.89, G.90, N.114, A.115, D.116, E.169, K.170, E.223, Q.247, K.249 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:I.56, E:I.56, E:L.89, E:G.90, E:A.115, E:D.116, E:D.116, E:E.169, E:Q.247 Salt bridges: E:K.13, E:E.85, E:K.170, E:K.249, E:K.249, E:K.249 GTP.6: 19 residues within 4Å: Chain F: L.6, V.7, G.8, G.9, Y.10, G.11, T.12, R.13, K.23, A.52, V.53, S.54, E.80, P.83, L.84, G.85, N.108, S.109, D.110 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:V.7, F:V.7, F:G.9, F:Y.10, F:T.12, F:T.12, F:R.13, F:A.52, F:L.84 Salt bridges: F:R.13, F:K.23, F:K.23, F:K.23, F:E.80 GTP.7: 17 residues within 4Å: Chain G: L.6, V.7, G.8, G.11, T.12, R.13, K.23, A.52, V.53, S.54, P.83, L.84, G.85, T.86, N.108, S.109, D.110 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:V.7, G:T.12, G:T.12, G:R.13, G:L.84, G:G.85, G:N.108, G:S.109, G:S.109 Salt bridges: G:R.13, G:R.13, G:K.23, G:K.23, G:K.23 GTP.8: 16 residues within 4Å: Chain H: L.6, V.7, G.8, R.13, K.23, E.80, L.84, G.85, T.86, P.89, N.108, S.109, D.110, D.218, G.220, Q.221 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:G.85, H:S.109, H:S.109, H:D.110, H:D.110, H:G.220 Salt bridges: H:R.13, H:K.23, H:K.23, H:E.80 GTP.9: 14 residues within 4Å: Chain I: L.6, V.7, G.8, G.9, G.11, T.12, R.13, K.23, S.54, G.85, P.89, N.108, S.109, D.110 14 PLIP interactions: 14 interactions with chain I Hydrogen bonds: I:G.11, I:T.12, I:T.12, I:T.12, I:R.13, I:S.54, I:G.85, I:G.85, I:S.109, I:D.110 Salt bridges: I:R.13, I:K.23, I:K.23, I:K.23 GTP.10: 19 residues within 4Å: Chain J: L.6, V.7, G.8, G.9, Y.10, G.11, T.12, R.13, K.23, A.52, V.53, S.54, E.80, P.83, L.84, G.85, N.108, S.109, D.110 17 PLIP interactions: 17 interactions with chain J Hydrogen bonds: J:G.8, J:G.9, J:T.12, J:T.12, J:R.13, J:S.54, J:L.84, J:G.85, J:S.109, J:D.110, J:D.110 Salt bridges: J:R.13, J:R.13, J:K.23, J:K.23, J:K.23, J:E.80 GTP.11: 18 residues within 4Å: Chain K: L.6, V.7, G.8, G.9, Y.10, G.11, T.12, R.13, K.23, A.52, V.53, E.80, P.83, G.85, T.86, N.108, S.109, D.110 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:G.8, K:G.9, K:Y.10, K:T.12, K:T.12, K:R.13, K:A.52, K:G.85, K:N.108, K:S.109 Salt bridges: K:K.23, K:K.23, K:K.23, K:E.80 GTP.12: 15 residues within 4Å: Chain L: L.6, V.7, G.8, A.52, V.53, S.54, G.85, T.86, N.108, D.110, N.172, G.174, E.194, W.216, D.218 8 PLIP interactions: 8 interactions with chain L Hydrogen bonds: L:V.7, L:G.8, L:N.108, L:D.110, L:N.172, L:N.172, L:D.218, L:D.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, L. et al., Cryo-EM structures of human GMPPA-GMPPB complex reveal how cells maintain GDP-mannose homeostasis. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-05-05

Peptides

Mannose-1-phosphate guanyltransferase alpha: ABDE
Mannose-1-phosphate guanyltransferase beta: CFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
C

E
D

C
E

F
F

G
G

H
I

I
J

J
K

K
L

L
H

Mannose-1-phosphate guanyltransferase alpha

Mannose-1-phosphate guanyltransferase beta

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