SMTL ID : 9uhs.1

Complete a6b6 of ATP-bound hPCC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.76 Å

Oligo State

hetero-6-6-6-mer

Ligands

6 x BTN: BIOTIN(Covalent)

BTN.1: 6 residues within 4Å: Chain A: G.144, R.399, Y.444, Y.445, D.446, K.694 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.446 Hydrogen bonds: A:R.399, A:D.446 BTN.5: 7 residues within 4Å: Chain D: Y.143, F.145, R.353, V.356, D.446, K.694 Ligands: BCT.8 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:D.446, D:K.694 Hydrogen bonds: D:D.446 BTN.10: 7 residues within 4Å: Chain G: Y.143, F.145, R.353, V.356, Y.445, D.446, K.694 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:D.446 Hydrogen bonds: G:R.353, G:D.446 BTN.14: 4 residues within 4Å: Chain J: F.145, R.353, D.446, K.694 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:D.446 Hydrogen bonds: J:R.353, J:D.446 BTN.18: 7 residues within 4Å: Chain M: Y.143, F.145, R.353, Y.445, D.446, K.694 Ligands: BCT.21 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:F.145, M:D.446 Hydrogen bonds: M:R.353, M:D.446 BTN.23: 4 residues within 4Å: Chain P: F.145, R.353, D.446, K.694 2 PLIP interactions: 2 interactions with chain P Hydrophobic interactions: P:F.145 Hydrogen bonds: P:D.446

6 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 22 residues within 4Å: Chain A: K.177, I.192, M.217, K.219, G.223, G.224, G.225, G.226, K.227, K.262, I.264, P.267, H.269, Q.293, N.296, E.336, L.338, L.348, E.349, N.351, T.501 Ligands: MG.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.219, A:G.223, A:G.225, A:G.226, A:K.227, A:K.262, A:I.264, A:Q.293, A:Q.293, A:E.349, A:N.351, A:N.351, A:T.501 Salt bridges: A:K.177, A:K.177, A:K.219, A:K.219 ATP.6: 16 residues within 4Å: Chain D: I.192, G.225, G.226, M.229, F.263, H.269, Q.293, N.296, E.336, L.338, L.348, E.349, N.351, R.353, T.501 Ligands: MG.7 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.225, D:H.269, D:Q.293, D:Q.293, D:E.349, D:N.351, D:R.353 ATP.11: 20 residues within 4Å: Chain G: I.192, M.217, G.224, G.225, G.226, M.229, K.262, F.263, I.264, P.267, H.269, Q.293, K.298, E.336, L.338, L.348, E.349, N.351, T.501 Ligands: MG.12 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:G.225, G:G.226, G:K.262, G:I.264, G:H.269, G:Q.293, G:N.351, G:T.501 Salt bridges: G:K.298 ATP.15: 19 residues within 4Å: Chain J: I.192, M.217, K.219, G.224, G.225, G.226, M.229, F.263, I.264, P.267, H.269, Q.293, E.336, L.338, L.348, E.349, N.351, T.501 Ligands: MG.16 13 PLIP interactions: 13 interactions with chain J Hydrogen bonds: J:K.219, J:K.219, J:G.225, J:G.226, J:I.264, J:Q.293, J:E.349, J:E.349, J:N.351, J:N.351, J:N.351, J:T.501, J:T.501 ATP.19: 20 residues within 4Å: Chain M: I.192, M.217, K.219, G.225, G.226, M.229, K.262, F.263, I.264, P.267, H.269, Q.293, E.336, L.338, L.348, E.349, N.351, T.501 Ligands: MG.20, BCT.21 11 PLIP interactions: 11 interactions with chain M Hydrogen bonds: M:K.219, M:G.225, M:G.226, M:K.262, M:I.264, M:Q.293, M:E.349, M:E.349, M:N.351, M:N.351, M:T.501 ATP.24: 18 residues within 4Å: Chain P: I.192, M.217, K.219, G.224, G.225, G.226, M.229, I.264, P.267, H.269, Q.293, E.336, L.338, L.348, E.349, N.351, T.501 Ligands: MG.25 7 PLIP interactions: 7 interactions with chain P Hydrogen bonds: P:G.225, P:G.226, P:Q.293, P:E.349, P:E.349, P:N.351, P:T.501

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.336, E.349 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.349 MG.7: 2 residues within 4Å: Chain D: E.336 Ligands: ATP.6 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.336, D:E.336 MG.12: 3 residues within 4Å: Chain G: E.336, E.349 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.349 MG.16: 3 residues within 4Å: Chain J: E.336, N.351 Ligands: ATP.15 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:E.336, J:E.336 MG.20: 3 residues within 4Å: Chain M: E.336, E.349 Ligands: ATP.19 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:E.336 MG.25: 2 residues within 4Å: Chain P: E.336 Ligands: ATP.24 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:E.336

6 x 1VU: propionyl Coenzyme A(Non-covalent)

1VU.4: 21 residues within 4Å: Chain B: G.144, G.145, V.170, I.179 Chain C: R.54, F.126, F.129, G.130, S.132, G.162, G.163, A.164, R.165, I.166, L.173, Y.176, P.199, A.201, G.202, G.203, Q.241 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.173, C:Y.176, B:I.179 Hydrogen bonds: C:S.132, C:G.162 Salt bridges: C:R.54 1VU.9: 17 residues within 4Å: Chain E: G.145, V.170, I.179 Chain F: R.54, R.61, F.129, G.130, S.132, G.162, G.163, A.164, R.165, I.166, P.199, G.202, G.203, Q.241 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:P.199, E:V.170 Hydrogen bonds: F:S.132, F:G.162, F:A.164, F:A.164, F:I.166, F:G.203 Salt bridges: F:R.54 1VU.13: 18 residues within 4Å: Chain H: G.144, G.145, V.170, M.171 Chain I: R.54, R.61, F.126, F.129, G.130, S.132, G.162, A.164, R.165, I.166, Y.176, G.202, G.203, Q.241 6 PLIP interactions: 5 interactions with chain I, 1 interactions with chain H Hydrophobic interactions: I:Y.176 Hydrogen bonds: I:R.61, I:S.132, I:A.164 Salt bridges: I:R.54, H:K.182 1VU.17: 16 residues within 4Å: Chain K: G.144, G.145, V.170, I.179 Chain L: R.54, F.126, F.129, G.130, S.132, G.162, G.163, A.164, P.199, G.202, G.203, Q.241 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:G.162, L:G.162 Salt bridges: L:R.54 Hydrophobic interactions: K:I.179 1VU.22: 17 residues within 4Å: Chain N: V.170 Chain O: R.54, R.61, F.126, F.129, G.130, S.132, G.162, G.163, A.164, L.173, Y.176, P.199, A.201, G.202, G.203, Q.241 10 PLIP interactions: 9 interactions with chain O, 1 interactions with chain N Hydrophobic interactions: O:A.164, O:L.173, O:Y.176, O:P.199, N:V.170 Hydrogen bonds: O:R.61, O:S.132, O:G.162, O:G.162 Salt bridges: O:R.54 1VU.26: 16 residues within 4Å: Chain Q: G.144, G.145, V.170 Chain R: R.54, R.61, F.129, G.130, S.132, G.162, A.164, R.165, I.166, L.173, Y.176, G.202, G.203 7 PLIP interactions: 7 interactions with chain R Hydrophobic interactions: R:L.173, R:Y.176 Hydrogen bonds: R:R.61, R:S.132, R:A.164, R:A.164 Salt bridges: R:R.54

2 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.8: 8 residues within 4Å: Chain D: K.298, N.351, R.353, Q.355, V.356, E.357, R.399 Ligands: BTN.5 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.298, D:Q.355, D:R.399 BCT.21: 7 residues within 4Å: Chain M: R.353, Q.355, V.356, E.357, R.399 Ligands: BTN.18, ATP.19 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:R.399, M:R.399

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, H. et al., Nanoscale conformational dynamics of human propionyl-CoA carboxylase. Structure (2025)

Release Date

2025-11-19

Peptides

Propionyl-CoA carboxylase alpha chain, mitochondrial: ADGJMP
Propionyl-CoA carboxylase beta chain, mitochondrial: BEHKNQ
Propionyl-CoA carboxylase beta chain, mitochondrial: CFILOR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

G
H

J
K

M
O

P
R

B
B

E
D

H
I

K
L

N
P

Q
S

C
F

F
G

I
J

L
M

O
Q

R
T

Propionyl-CoA carboxylase alpha chain, mitochondrial

Propionyl-CoA carboxylase beta chain, mitochondrial

Propionyl-CoA carboxylase beta chain, mitochondrial

Related Entries With Identical Sequence