SMTL ID : 2zah.2 (4 other biounits)

X-ray structure of Melon necrotic spot virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

homo-15-mer

Ligands

20 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.87, Q.201 Chain C: D.115, D.120 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:D.115, C:D.115, C:D.120, A:D.87 CA.3: 4 residues within 4Å: Chain A: D.115, D.120 Chain B: D.87, Q.201 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Metal complexes: B:D.87, A:D.115, A:D.115, A:D.120 CA.4: 5 residues within 4Å: Chain B: D.117, D.120 Chain C: D.87, D.159, Q.201 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Metal complexes: B:D.117, B:D.120, B:D.120, C:D.87, C:D.159 CA.5: 4 residues within 4Å: Chain B: D.115, D.120 Chain C: D.87, Q.201 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:D.115, B:D.115, B:D.120, C:D.87 CA.6: 4 residues within 4Å: Chain D: D.87, Q.201 Chain F: D.115, D.120 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Metal complexes: F:D.115, F:D.115, F:D.120, D:D.87 CA.8: 4 residues within 4Å: Chain D: D.115, D.120 Chain E: D.87, Q.201 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Metal complexes: D:D.115, D:D.115, D:D.120, E:D.87 CA.9: 5 residues within 4Å: Chain E: D.117, D.120 Chain F: D.87, D.159, Q.201 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Metal complexes: F:D.87, F:D.159, E:D.117, E:D.120, E:D.120 CA.10: 4 residues within 4Å: Chain E: D.115, D.120 Chain F: D.87, Q.201 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Metal complexes: E:D.115, E:D.115, E:D.120, F:D.87 CA.11: 4 residues within 4Å: Chain G: D.87, Q.201 Chain I: D.115, D.120 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain G Metal complexes: I:D.115, I:D.115, I:D.120, G:D.87 CA.13: 4 residues within 4Å: Chain G: D.115, D.120 Chain H: D.87, Q.201 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H Metal complexes: G:D.115, G:D.115, G:D.120, H:D.87 CA.14: 5 residues within 4Å: Chain H: D.117, D.120 Chain I: D.87, D.159, Q.201 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain I Metal complexes: H:D.117, H:D.120, H:D.120, I:D.87, I:D.159 CA.15: 4 residues within 4Å: Chain H: D.115, D.120 Chain I: D.87, Q.201 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain I Metal complexes: H:D.115, H:D.115, H:D.120, I:D.87, I:D.87 CA.16: 4 residues within 4Å: Chain J: D.87, Q.201 Chain L: D.115, D.120 4 PLIP interactions: 1 interactions with chain J, 3 interactions with chain L Metal complexes: J:D.87, L:D.115, L:D.115, L:D.120 CA.18: 4 residues within 4Å: Chain J: D.115, D.120 Chain K: D.87, Q.201 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain K Metal complexes: J:D.115, J:D.115, J:D.120, K:D.87 CA.19: 5 residues within 4Å: Chain K: D.117, D.120 Chain L: D.87, D.159, Q.201 5 PLIP interactions: 3 interactions with chain K, 2 interactions with chain L Metal complexes: K:D.117, K:D.120, K:D.120, L:D.87, L:D.159 CA.20: 4 residues within 4Å: Chain K: D.115, D.120 Chain L: D.87, Q.201 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain L Metal complexes: K:D.115, K:D.115, K:D.120, L:D.87 CA.21: 4 residues within 4Å: Chain M: D.87, Q.201 Chain O: D.115, D.120 4 PLIP interactions: 3 interactions with chain O, 1 interactions with chain M Metal complexes: O:D.115, O:D.115, O:D.120, M:D.87 CA.23: 4 residues within 4Å: Chain M: D.115, D.120 Chain N: D.87, Q.201 4 PLIP interactions: 1 interactions with chain N, 3 interactions with chain M Metal complexes: N:D.87, M:D.115, M:D.115, M:D.120 CA.24: 5 residues within 4Å: Chain N: D.117, D.120 Chain O: D.87, D.159, Q.201 5 PLIP interactions: 3 interactions with chain N, 2 interactions with chain O Metal complexes: N:D.117, N:D.120, N:D.120, O:D.87, O:D.159 CA.25: 4 residues within 4Å: Chain N: D.115, D.120 Chain O: D.87, Q.201 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain O Metal complexes: N:D.115, N:D.115, N:D.120, O:D.87

5 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 4 residues within 4Å: Ligands: UNX.7, UNX.12, UNX.17, UNX.22 No protein-ligand interaction detected (PLIP) UNX.7: 4 residues within 4Å: Ligands: UNX.2, UNX.12, UNX.17, UNX.22 No protein-ligand interaction detected (PLIP) UNX.12: 4 residues within 4Å: Ligands: UNX.2, UNX.7, UNX.17, UNX.22 No protein-ligand interaction detected (PLIP) UNX.17: 4 residues within 4Å: Ligands: UNX.2, UNX.7, UNX.12, UNX.22 No protein-ligand interaction detected (PLIP) UNX.22: 4 residues within 4Å: Ligands: UNX.2, UNX.7, UNX.12, UNX.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wada, Y. et al., X-ray structure of Melon necrotic spot virus. Acta Crystallogr.,Sect.F (2008)

Release Date

2008-10-07

Peptides

Coat protein: ABCDEFGHIJKLMNO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

M
A

N
B

O
C

Coat protein

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